From 7da9dbfaa76f27526bee9c7266993395e3d5a304 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 20:47:59 +0100 Subject: [PATCH 1/7] commit original vcf_2_decifer.py from decifer repo --- scripts/vafator2decifer.py | 236 +++++++++++++++++++++++++++++++++++++ 1 file changed, 236 insertions(+) create mode 100644 scripts/vafator2decifer.py diff --git a/scripts/vafator2decifer.py b/scripts/vafator2decifer.py new file mode 100644 index 0000000..4e6cfef --- /dev/null +++ b/scripts/vafator2decifer.py @@ -0,0 +1,236 @@ +#!/usr/bin/python -tt + +""" +Please type "python3 vcf_2_decifer.py --help" for a the full list of options + +This is a python script that takes as input (1) a multi-sample VCF, e.g. variants called in multiple tumor samples from a single patient, (2) a file containing copy number aberration information, e.g. the "best.seg.ucn" file that is output by the program HATCHet. The sample names must agree in both files! + +This script also uses cyvcf2 to parse VCF files efficiently, and the python implementation of bedtools to find which CNA interval each SNV overlaps with. Please make a conda environment containing these python modules before running this script. +For instance, do the following to run this script: + +conda create -n vcf_bedtools pybedtools cyvcf2 pandas -y +conda activate vcf_bedtools +python vcf_2_decifer.py [OPTIONS] +""" + +import re +import sys +import pybedtools as pbt +from cyvcf2 import VCF +import os +import pandas as pd +import numpy as np +from collections import defaultdict +import argparse + + +def filterByDepth(gt_depths, gt_alt_depths, Filter): + PASS = 1 + missing = 0 + for i in range(len(gt_depths)): + # filter if genotype has low depth or is missing + if (gt_depths[i] < Filter['MinDepth']): + missing += 1 + # filter if alt allele isn't greater than the specified threshold in at least one sample + if not any(np.greater_equal(gt_alt_depths, Filter['MinDepthAltAllele'])): + missing += 1 + # (gt_alt_depths[i] < Filter['MinDepthAltAllele']) + if missing > 0: + PASS = 0 + return (PASS) + + +def compute_ref_var_depths(vcf, FilterDP): + ref_var_depths = defaultdict( + list) # ref_var_depths[char_label] = list of (ref,alt) tuples, one for each sample, in same order as vcf.samples + for variant in vcf: + if len(variant.ALT) == 1 and variant.var_type == "snp": + PASS = filterByDepth(variant.gt_depths, variant.gt_alt_depths, FilterDP) + # print(np.greater_equal(variant.gt_alt_depths,FilterDP['MinDepthAltAllele'])) + if PASS: + chrom = variant.CHROM + pos = variant.end + char_label = ".".join(map(str, [chrom, pos, variant.REF, variant.ALT[0]])) + + for i in range(len(vcf.samples)): + ref = variant.gt_depths[i] - variant.gt_alt_depths[i] + alt = variant.gt_alt_depths[i] + ref_var_depths[char_label].append((ref, alt)) + return (ref_var_depths) + + +def print_output(vcf, ref_var_depths, cna_overlaps, outdir): + char_index = 0 + chars = ref_var_depths.keys() & cna_overlaps.keys() + header = [str(len(chars)) + " #characters"] + header.append(str(len(vcf.samples)) + " #samples") + header.append("#sample_index\tsample_label\tcharacter_index\tcharacter_label\tref\tvar") + print(header) + with open(f"{outdir}/decifer.input.tsv", 'w') as out: + print("\n".join(header), file=out) + for char_label in ref_var_depths: + if char_label in cna_overlaps: + for i in range(len(vcf.samples)): + r, v = ref_var_depths[char_label][i][0], ref_var_depths[char_label][i][1] + to_print = [i, vcf.samples[i], char_index, char_label, r, v] + cnas = cna_overlaps[char_label][i] + to_print.extend(cnas) + print("\t".join(map(str, to_print)), file=out) + # print(i, vcf.samples[i], char_index, char_label, r, v) + char_index += 1 + + +def print_purities(cna_df, sample_index, num_samples, outdir): + purities = {} + for i, row in cna_df.head(num_samples + 1).iterrows(): + purities[row['SAMPLE']] = 1.0 - row['u_normal'] + with open(f"{outdir}/decifer.purity.tsv", 'w') as out: + for sample in sample_index: + print(sample_index[sample], purities[sample], file=out, sep="\t") + + +def filter_high_CN_sites(cn_states_persite, max_CN): + # returns 0 if site has CN state greater than max_CN + # cn_states_persite is a list of str "A|B", CN states of maternal/paternal chromosomes + for i in cn_states_persite: + j = i.split("|") + if int(j[0]) + int(j[1]) > max_CN: + return 0 + return 1 + + +def print_unique_CN_states(cn_states, max_CN, outdir): + # print unique copy number states for sites that are below the max_CN threshold + cn_states = tuple(set(cn_states)) + with open(f"{outdir}/cn_states.txt", 'w') as out: + for value in cn_states: + PASS = 1 + for i in value: + if int(i[0]) + int(i[1]) > max_CN: + PASS = 0 + if PASS: + out.write(';'.join([','.join(i) for i in value]) + '\n') + + +def print_filtered_sites(filtered_sites, cna_overlaps, outdir): + with open(f"{outdir}/filtered_sites.txt", 'w') as out: + out.write("\n".join(filtered_sites)) + print(file=out) + with open(f"{outdir}/filtered_stats.txt", 'w') as out: + filtered = len(filtered_sites) + total = len(cna_overlaps.keys()) + print("# sites that were filtered due to copy-number states > max_CN", file=out) + print("filtered: ", filtered, file=out) + print("fraction: ", float(filtered / total), file=out) + + +def overlap_cna_snp(vcf_samples, max_CN, out_dir): + cna_overlaps = defaultdict(list) + cn_states_allsites = [] # a list of tuples + filtered_sites = set() # sites filtered out because of high CN + snps = pbt.BedTool(f"{out_dir}/snps.bed") + # for each sample in VCF, intersect it's SNVs with sample-specific CNAs + for sample in vcf_samples: + sample_cnas = pbt.BedTool(f"{out_dir}/{sample}_cna.bed") + # snps.intersect(sample_cnas, wo=True).saveas(f"snps_cnas_overlap_{sample}.bed") + bed = snps.intersect(sample_cnas, wo=True) + for line in bed: + line = str(line).split() + # first 5 columns are SNP info (chr,pos_start,pos_end,REF,ALT), rest are CNA info + # CNA info starts with CHR, START, END, which you don't want, so start at index 8 + # exclude the last index, since bedtools adds this, the number of bp of overlap + char_label = ".".join([line[0], line[2], line[3], line[4]]) + cns = line[8:-1:2] # copy-number states, string[start:end:step] + props = line[9:-1:2] # copy-number proportions + if len(cns) != len(props): + sys.exit("CNA file not formatted correctly!") + + cn_info = defaultdict(float) # dict with cn_info["A|B"] = proportion + for c, p in zip(cns, props): + cn_info[c] += float(p) # this collapses nonunique CN states + + # returns 0 if CN state too high + if filter_high_CN_sites(cn_info.keys(), max_CN): + # store results, converting from dict to a list for later printing + cna_info = [] + [cna_info.extend([c.split("|")[0], c.split("|")[1], cn_info[c]]) for c in cn_info] + cna_overlaps[char_label].append(cna_info) + else: + filtered_sites.add(char_label) + # get collection of unique CN states for this SNV site + tuple_states = [(c.split("|")[0], c.split("|")[1]) for c in cn_info] + cn_states_allsites.append(tuple(set(tuple_states))) + + return cna_overlaps, cn_states_allsites, filtered_sites + + +def main(): + parser = argparse.ArgumentParser(description='Generate input for Decifer using VCF file and HATCHet CNA file') + parser.add_argument("-V", "--vcf_file", required=True, type=str, help="single or multi-sample VCF file") + parser.add_argument("-C", "--cna_file", required=True, type=str, help="HATCHet CNA file: best.seg.ucn ") + parser.add_argument("-O", "--out_dir", required=True, default="./", type=str, + help="directory for printing files; please make unique for each patient!") + parser.add_argument("-M", "--min_depth", required=True, type=int, help="minimum depth PER sample") + parser.add_argument("-A", "--min_alt_depth", required=True, type=int, + help="minimum depth of ALT allele in at least one sample") + parser.add_argument("-N", "--max_CN", required=False, default=6, type=int, + help="maximum total copy number for each observed clone") + args = parser.parse_args() + + vcf_name = os.path.basename(args.vcf_file) + vcf = VCF(args.vcf_file, gts012=True) + + # Filtering criteria + FilterDP = {} + FilterDP['MinDepth'] = args.min_depth + FilterDP['MinDepthAltAllele'] = args.min_alt_depth + + num_samples = len(vcf.samples) + sample_index = {vcf.samples[i]: i for i in range(len(vcf.samples))} + print(vcf.samples) + print(type(vcf.samples)) + + # ref_var_depths[char_label] = list of (ref,alt) tuples, one for each sample, in same order as vcf.samples + ref_var_depths = compute_ref_var_depths(vcf, FilterDP) + + # print BED file for SNPs + with open(f"{args.out_dir}/snps.bed", 'w') as out: + print("chrom\tstart\tend\tREF\tALT", file=out) + for chr_label in ref_var_depths: + pos = chr_label.split(".") + # subtract 1 from position to create interval in BED format + print(pos[0], int(pos[1]) - 1, int(pos[1]), pos[2], pos[3], sep="\t", file=out) + + # Load in CNA information + cna_df = pd.read_csv(args.cna_file, sep='\t', index_col=False) + # print purity information + print_purities(cna_df, sample_index, num_samples, args.out_dir) + + # prepare BED files for CNA intervals for each sample, for overlapping with SNPs + for sample in vcf.samples: + df = cna_df[cna_df['SAMPLE'] == sample] + # consider subtracting 1 from start of interval to be compatible with BED format, leave end interval alone + df.loc[:, 'START'] = df['START'] + df = df.drop('SAMPLE', axis=1) + df.to_csv(f"{args.out_dir}/{sample}_cna.bed", index=False, sep="\t") + + # overlap SNPs with CNA intervals for each sample + # cna_overlaps[char_label] = list of tuples of CNA info (one tuple for each sample, in same order as vcf.samples) + # this function also prints the observed CN state trees for the generatestatetrees function + cna_overlaps, cn_states_allsites, filtered_sites = overlap_cna_snp(vcf.samples, args.max_CN, args.out_dir) + + # sites may have unique CN states that are duplicate; set them to find unique CN states across sites + print_unique_CN_states(cn_states_allsites, args.max_CN, args.out_dir) + print_filtered_sites(filtered_sites, cna_overlaps, args.out_dir) + + print_output(vcf, ref_var_depths, cna_overlaps, args.out_dir) + + os.system(f"rm {args.out_dir}/snps.bed") + for sample in vcf.samples: + os.system(f"rm {args.out_dir}/{sample}_cna.bed") + + +if __name__ == '__main__': + main() + + From 6e5d85da3fd40dfd4012c9cd5082aab9556f52ba Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 21:09:08 +0100 Subject: [PATCH 2/7] pass list of samples to vafator2decifer.py --- scripts/vafator2decifer.py | 55 +++++++++++++++++++------------------- 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/scripts/vafator2decifer.py b/scripts/vafator2decifer.py index 4e6cfef..bcb9f98 100644 --- a/scripts/vafator2decifer.py +++ b/scripts/vafator2decifer.py @@ -16,7 +16,7 @@ import re import sys import pybedtools as pbt -from cyvcf2 import VCF +from cyvcf2 import VCF, Variant import os import pandas as pd import numpy as np @@ -24,39 +24,37 @@ import argparse -def filterByDepth(gt_depths, gt_alt_depths, Filter): +def filterByDepth(variant: Variant, Filter, samples): PASS = 1 missing = 0 - for i in range(len(gt_depths)): + for s in samples: # filter if genotype has low depth or is missing - if (gt_depths[i] < Filter['MinDepth']): - missing += 1 - # filter if alt allele isn't greater than the specified threshold in at least one sample - if not any(np.greater_equal(gt_alt_depths, Filter['MinDepthAltAllele'])): + if variant.INFO["{}_dp".format(s)] < Filter['MinDepth']: missing += 1 + # filter if alt allele isn't greater than the specified threshold in at least one sample + if not any(np.greater_equal([variant.INFO["{}_ac".format(s)] for s in samples], Filter['MinDepthAltAllele'])): + missing += 1 # (gt_alt_depths[i] < Filter['MinDepthAltAllele']) if missing > 0: PASS = 0 return (PASS) -def compute_ref_var_depths(vcf, FilterDP): - ref_var_depths = defaultdict( - list) # ref_var_depths[char_label] = list of (ref,alt) tuples, one for each sample, in same order as vcf.samples +def compute_ref_var_depths(vcf, FilterDP, samples): + ref_var_depths = defaultdict(list) + # ref_var_depths[char_label] = list of (ref,alt) tuples, one for each sample, in same order as vcf.samples + variant: Variant for variant in vcf: if len(variant.ALT) == 1 and variant.var_type == "snp": - PASS = filterByDepth(variant.gt_depths, variant.gt_alt_depths, FilterDP) + PASS = filterByDepth(variant, FilterDP, samples) # print(np.greater_equal(variant.gt_alt_depths,FilterDP['MinDepthAltAllele'])) if PASS: - chrom = variant.CHROM - pos = variant.end - char_label = ".".join(map(str, [chrom, pos, variant.REF, variant.ALT[0]])) - - for i in range(len(vcf.samples)): - ref = variant.gt_depths[i] - variant.gt_alt_depths[i] - alt = variant.gt_alt_depths[i] + char_label = ".".join(map(str, [variant.CHROM, variant.POS, variant.REF, variant.ALT[0]])) + for s in samples: + alt = variant.INFO["{}_ac".format(s)] + ref = variant.INFO["{}_dp".format(s)] - alt ref_var_depths[char_label].append((ref, alt)) - return (ref_var_depths) + return ref_var_depths def print_output(vcf, ref_var_depths, cna_overlaps, outdir): @@ -167,6 +165,10 @@ def overlap_cna_snp(vcf_samples, max_CN, out_dir): def main(): parser = argparse.ArgumentParser(description='Generate input for Decifer using VCF file and HATCHet CNA file') parser.add_argument("-V", "--vcf_file", required=True, type=str, help="single or multi-sample VCF file") + parser.add_argument("-S", "--samples", required=True, type=str, + help="comma separated list of sample name prefixes to use for VAFator annotations, " + "eg: primary_tumor,metastasis_tumor; the annotations primary_tumor_ac, primary_tumor_dp, " + "etc. will be expected to exist") parser.add_argument("-C", "--cna_file", required=True, type=str, help="HATCHet CNA file: best.seg.ucn ") parser.add_argument("-O", "--out_dir", required=True, default="./", type=str, help="directory for printing files; please make unique for each patient!") @@ -185,13 +187,12 @@ def main(): FilterDP['MinDepth'] = args.min_depth FilterDP['MinDepthAltAllele'] = args.min_alt_depth - num_samples = len(vcf.samples) - sample_index = {vcf.samples[i]: i for i in range(len(vcf.samples))} - print(vcf.samples) - print(type(vcf.samples)) + samples = args.samples.split(",") + num_samples = len(samples) + sample_index = {samples[i]: i for i in range(len(samples))} # ref_var_depths[char_label] = list of (ref,alt) tuples, one for each sample, in same order as vcf.samples - ref_var_depths = compute_ref_var_depths(vcf, FilterDP) + ref_var_depths = compute_ref_var_depths(vcf, FilterDP, samples) # print BED file for SNPs with open(f"{args.out_dir}/snps.bed", 'w') as out: @@ -207,7 +208,7 @@ def main(): print_purities(cna_df, sample_index, num_samples, args.out_dir) # prepare BED files for CNA intervals for each sample, for overlapping with SNPs - for sample in vcf.samples: + for sample in samples: df = cna_df[cna_df['SAMPLE'] == sample] # consider subtracting 1 from start of interval to be compatible with BED format, leave end interval alone df.loc[:, 'START'] = df['START'] @@ -217,7 +218,7 @@ def main(): # overlap SNPs with CNA intervals for each sample # cna_overlaps[char_label] = list of tuples of CNA info (one tuple for each sample, in same order as vcf.samples) # this function also prints the observed CN state trees for the generatestatetrees function - cna_overlaps, cn_states_allsites, filtered_sites = overlap_cna_snp(vcf.samples, args.max_CN, args.out_dir) + cna_overlaps, cn_states_allsites, filtered_sites = overlap_cna_snp(samples, args.max_CN, args.out_dir) # sites may have unique CN states that are duplicate; set them to find unique CN states across sites print_unique_CN_states(cn_states_allsites, args.max_CN, args.out_dir) @@ -226,7 +227,7 @@ def main(): print_output(vcf, ref_var_depths, cna_overlaps, args.out_dir) os.system(f"rm {args.out_dir}/snps.bed") - for sample in vcf.samples: + for sample in samples: os.system(f"rm {args.out_dir}/{sample}_cna.bed") From cd77a8d7b564e98d4968e4fe8c88021ed3ea1ca6 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 21:19:32 +0100 Subject: [PATCH 3/7] add vafator2decifer as a CLI command --- setup.py | 3 ++- vafator/command_line.py | 21 ++++++++++++++++++++- {scripts => vafator}/vafator2decifer.py | 23 +---------------------- 3 files changed, 23 insertions(+), 24 deletions(-) rename {scripts => vafator}/vafator2decifer.py (87%) diff --git a/setup.py b/setup.py index 753dde5..2ec46f6 100755 --- a/setup.py +++ b/setup.py @@ -20,7 +20,8 @@ entry_points={ 'console_scripts': [ 'vafator=vafator.command_line:annotator', - 'multiallelics-filter=vafator.command_line:multiallelics_filter' + 'multiallelics-filter=vafator.command_line:multiallelics_filter', + 'vafator2decifer=vafator.command_line:vafator2decifer' ], }, author="TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz" diff --git a/vafator/command_line.py b/vafator/command_line.py index 7229ce1..51a198e 100755 --- a/vafator/command_line.py +++ b/vafator/command_line.py @@ -5,7 +5,7 @@ import vafator from vafator.annotator import Annotator from vafator.multiallelic_filter import MultiallelicFilter - +from vafator.vafator2decifer import run_vafator2decifer epilog = "Copyright (c) 2019-2021 TRON gGmbH (See LICENSE for licensing details)" @@ -72,3 +72,22 @@ def multiallelics_filter(): logging.error(str(e)) sys.exit(-1) logging.info("Vafator multiallelic filter finished!") + + +def vafator2decifer(): + parser = argparse.ArgumentParser(description='Generate input for Decifer using VCF file and HATCHet CNA file') + parser.add_argument("-V", "--vcf_file", required=True, type=str, help="single or multi-sample VCF file") + parser.add_argument("-S", "--samples", required=True, type=str, + help="comma separated list of sample name prefixes to use for VAFator annotations, " + "eg: primary_tumor,metastasis_tumor; the annotations primary_tumor_ac, primary_tumor_dp, " + "etc. will be expected to exist") + parser.add_argument("-C", "--cna_file", required=True, type=str, help="HATCHet CNA file: best.seg.ucn ") + parser.add_argument("-O", "--out_dir", required=True, default="./", type=str, + help="directory for printing files; please make unique for each patient!") + parser.add_argument("-M", "--min_depth", required=True, type=int, help="minimum depth PER sample") + parser.add_argument("-A", "--min_alt_depth", required=True, type=int, + help="minimum depth of ALT allele in at least one sample") + parser.add_argument("-N", "--max_CN", required=False, default=6, type=int, + help="maximum total copy number for each observed clone") + args = parser.parse_args() + run_vafator2decifer(args) diff --git a/scripts/vafator2decifer.py b/vafator/vafator2decifer.py similarity index 87% rename from scripts/vafator2decifer.py rename to vafator/vafator2decifer.py index bcb9f98..69079b2 100644 --- a/scripts/vafator2decifer.py +++ b/vafator/vafator2decifer.py @@ -162,22 +162,7 @@ def overlap_cna_snp(vcf_samples, max_CN, out_dir): return cna_overlaps, cn_states_allsites, filtered_sites -def main(): - parser = argparse.ArgumentParser(description='Generate input for Decifer using VCF file and HATCHet CNA file') - parser.add_argument("-V", "--vcf_file", required=True, type=str, help="single or multi-sample VCF file") - parser.add_argument("-S", "--samples", required=True, type=str, - help="comma separated list of sample name prefixes to use for VAFator annotations, " - "eg: primary_tumor,metastasis_tumor; the annotations primary_tumor_ac, primary_tumor_dp, " - "etc. will be expected to exist") - parser.add_argument("-C", "--cna_file", required=True, type=str, help="HATCHet CNA file: best.seg.ucn ") - parser.add_argument("-O", "--out_dir", required=True, default="./", type=str, - help="directory for printing files; please make unique for each patient!") - parser.add_argument("-M", "--min_depth", required=True, type=int, help="minimum depth PER sample") - parser.add_argument("-A", "--min_alt_depth", required=True, type=int, - help="minimum depth of ALT allele in at least one sample") - parser.add_argument("-N", "--max_CN", required=False, default=6, type=int, - help="maximum total copy number for each observed clone") - args = parser.parse_args() +def run_vafator2decifer(args): vcf_name = os.path.basename(args.vcf_file) vcf = VCF(args.vcf_file, gts012=True) @@ -229,9 +214,3 @@ def main(): os.system(f"rm {args.out_dir}/snps.bed") for sample in samples: os.system(f"rm {args.out_dir}/{sample}_cna.bed") - - -if __name__ == '__main__': - main() - - From 63f50323854c0172de1e34a555f6c57581d6fec5 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 21:19:53 +0100 Subject: [PATCH 4/7] add vafator2decifer as a CLI command --- vafator/command_line.py | 1 + 1 file changed, 1 insertion(+) diff --git a/vafator/command_line.py b/vafator/command_line.py index 51a198e..a1765c7 100755 --- a/vafator/command_line.py +++ b/vafator/command_line.py @@ -49,6 +49,7 @@ def annotator(): sys.exit(-1) logging.info("Vafator finished!") + def multiallelics_filter(): # set up logger From d672343098a6ac01f6b9d32b38dadcf8f8ae00ff Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 22:39:42 +0100 Subject: [PATCH 5/7] add more flexible parameter --bam and remove --prefix --- nf_modules/vafator.nf | 4 +- requirements.txt | 3 +- vafator/__init__.py | 2 +- vafator/annotator.py | 188 +++++++----------- vafator/command_line.py | 35 +++- vafator/pileups.py | 45 ++++- ...c.snps.indels.chr1_1000000_2000000.vaf.vcf | 114 +++++------ .../tests/resources/results/test1_output.vcf | 2 +- .../tests/resources/results/test2_output.vcf | 2 +- .../tests/resources/results/test3_output.vcf | 2 +- .../tests/resources/results/test4_output.vcf | 2 +- .../tests/resources/results/test5_output.vcf | 2 +- .../results/test_annotator1_output.vcf | 54 ++--- vafator/tests/test_annotator.py | 11 +- 14 files changed, 230 insertions(+), 236 deletions(-) diff --git a/nf_modules/vafator.nf b/nf_modules/vafator.nf index f3542f1..8f75357 100644 --- a/nf_modules/vafator.nf +++ b/nf_modules/vafator.nf @@ -14,7 +14,7 @@ process VAFATOR { tag "${name}" publishDir "${params.output}/${name}", mode: "copy" - conda (params.enable_conda ? "bioconda::vafator=1.0.0" : null) + conda (params.enable_conda ? "bioconda::vafator=1.1.0" : null) input: tuple val(name), file(vcf), val(normal_bams), val(tumor_bams) @@ -42,7 +42,7 @@ process MULTIALLELIC_FILTER { tag "${name}" publishDir "${params.output}/${name}", mode: "copy" - conda (params.enable_conda ? "bioconda::vafator=1.0.0" : null) + conda (params.enable_conda ? "bioconda::vafator=1.1.0" : null) input: tuple val(name), file(vcf) diff --git a/requirements.txt b/requirements.txt index 0e1db71..f734b0a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,5 @@ pandas==1.3.3 pysam==0.17.0 cyvcf2==0.30.11 -logzero==1.7.0 \ No newline at end of file +logzero==1.7.0 +pybedtools==0.8.2 \ No newline at end of file diff --git a/vafator/__init__.py b/vafator/__init__.py index de36010..dceeaa2 100755 --- a/vafator/__init__.py +++ b/vafator/__init__.py @@ -1 +1 @@ -VERSION='1.0.0' \ No newline at end of file +VERSION='1.1.0' \ No newline at end of file diff --git a/vafator/annotator.py b/vafator/annotator.py index cb8f24e..fbe5a8a 100755 --- a/vafator/annotator.py +++ b/vafator/annotator.py @@ -1,13 +1,10 @@ -from typing import List import pysam from cyvcf2 import VCF, Writer, Variant import os -from pysam import AlignmentFile import vafator import datetime import json -from vafator.pileups import get_insertion_metrics, get_deletion_metrics, get_snv_metrics, get_variant_pileup, \ - build_variant +from vafator.pileups import get_variant_pileup, build_variant, get_metrics class Annotator(object): @@ -19,8 +16,7 @@ class Annotator(object): "timestamp": datetime.datetime.now().timestamp(), } - def __init__(self, input_vcf: str, output_vcf: str, normal_bams=[], tumor_bams=[], - mapping_qual_thr=0, base_call_qual_thr=29, prefix=None): + def __init__(self, input_vcf: str, output_vcf: str, input_bams: dict, mapping_qual_thr=0, base_call_qual_thr=29): self.mapping_quality_threshold = mapping_qual_thr self.base_call_quality_threshold = base_call_qual_thr @@ -28,124 +24,85 @@ def __init__(self, input_vcf: str, output_vcf: str, normal_bams=[], tumor_bams=[ # sets a line in the header with the command used to annotate the file self.vafator_header["input_vcf"] = input_vcf self.vafator_header["output_vcf"] = output_vcf - self.vafator_header["normal_bams"] = normal_bams - self.vafator_header["tumor_bams"] = tumor_bams + self.vafator_header["bams"] = ";".join(["{}:{}".format(s, ",".join(b)) for s, b in input_bams.items()]) self.vafator_header["mapping_quality_threshold"] = mapping_qual_thr self.vafator_header["base_call_quality_threshold"] = base_call_qual_thr - self.vafator_header["prefix"] = prefix self.vcf.add_to_header("##vafator_command_line={}".format(json.dumps(self.vafator_header))) # adds to the header all the names of the annotations - self.tumor_prefix = "{prefix}_tumor".format(prefix=prefix) if prefix is not None else "tumor" - self.normal_prefix = "{prefix}_normal".format(prefix=prefix) if prefix is not None else "normal" - for a in Annotator._get_headers(self.tumor_prefix, tumor_bams) + \ - Annotator._get_headers(self.normal_prefix, normal_bams): + for a in Annotator._get_headers(input_bams): self.vcf.add_info_to_header(a) self.vcf_writer = Writer(output_vcf, self.vcf) - self.tumor_bams = [pysam.AlignmentFile(b, "rb") for b in tumor_bams] - self.normal_bams = [pysam.AlignmentFile(b, "rb") for b in normal_bams] + self.bam_readers = {s : [pysam.AlignmentFile(b, "rb") for b in bams] for s, bams in input_bams.items()} @staticmethod - def _get_headers(prefix, bams): + def _get_headers(input_bams: dict): headers = [] - if len(bams) > 0: - headers = [ - {'ID': "{}_af".format(prefix), - 'Description': "Allele frequency for the alternate alleles in the {} samples".format(prefix), - 'Type': 'Float', 'Number': 'A'}, - {'ID': "{}_dp".format(prefix), - 'Description': "Total depth of coverage in the {} samples (independent of alleles)".format(prefix), - 'Type': 'Float', 'Number': 'A'}, - {'ID': "{}_ac".format(prefix), - 'Description': "Allele count for the alternate alleles in the {} samples".format(prefix), - 'Type': 'Integer', 'Number': 'A'} - ] - if len(bams) > 1: - for i, b in enumerate(bams, start=1): - n = os.path.basename(b).split(".")[0] - headers = headers + [ - {'ID': "{}_af_{}".format(prefix, i), - 'Description': "Allele frequency for the alternate alleles in the {} sample {}".format(prefix, n), - 'Type': 'Float', 'Number': 'A'}, - {'ID': "{}_dp_{}".format(prefix, i), - 'Description': "Depth of coverage in the {} sample {} (independent of alleles)".format(prefix, n), - 'Type': 'Float', 'Number': 'A'}, - {'ID': "{}_ac_{}".format(prefix, i), - 'Description': "Allele count for the alternate alleles in the {} sample {}".format(prefix, n), - 'Type': 'Integer', 'Number': 'A'} - ] + + for s, bams in input_bams.items(): + headers.append({ + 'ID': "{}_af".format(s), + 'Description': "Allele frequency for the alternate alleles in the {} sample/s".format(s), + 'Type': 'Float', + 'Number': 'A' + }) + headers.append({ + 'ID': "{}_dp".format(s), + 'Description': "Total depth of coverage in the {} sample/s (independent of alleles)".format(s), + 'Type': 'Float', + 'Number': '1' + }) + headers.append({ + 'ID': "{}_ac".format(s), + 'Description': "Allele count for the alternate alleles in the {} sample/s".format(s), + 'Type': 'Integer', + 'Number': 'A' + }) + + if len(bams) > 1: + for i, bam in enumerate(bams, start=1): + n = os.path.basename(bam).split(".")[0] + headers = headers + [ + {'ID': "{}_af_{}".format(s, i), + 'Description': "Allele frequency for the alternate alleles in the {} sample {}".format(s, n), + 'Type': 'Float', 'Number': 'A'}, + {'ID': "{}_dp_{}".format(s, i), + 'Description': "Depth of coverage in the {} sample {} (independent of alleles)".format(s, n), + 'Type': 'Float', 'Number': '1'}, + {'ID': "{}_ac_{}".format(s, i), + 'Description': "Allele count for the alternate alleles in the {} sample {}".format(s, n), + 'Type': 'Integer', 'Number': 'A'} + ] return headers def _write_batch(self, batch): for v in batch: self.vcf_writer.write_record(v) - def _add_snv_stats(self, bams: List[AlignmentFile], variant: Variant, prefix: str): + def _add_stats(self, variant: Variant): global_dp = 0 global_ac = {} vafator_variant = build_variant(variant) - for i, b in enumerate(bams): - pileups = get_variant_pileup(variant=vafator_variant, bam=b, - min_base_quality=self.base_call_quality_threshold, - min_mapping_quality=self.mapping_quality_threshold) - ac, dp = get_snv_metrics(variant=vafator_variant, pileups=pileups) - if len(bams) > 1: - variant.INFO["{}_af_{}".format(prefix, i + 1)] = ",".join( - [str(self._calculate_af(ac[alt], dp)) for alt in variant.ALT]) - variant.INFO["{}_ac_{}".format(prefix, i + 1)] = ",".join([str(ac[alt]) for alt in variant.ALT]) - variant.INFO["{}_dp_{}".format(prefix, i + 1)] = dp - for alt in variant.ALT: - global_ac[alt] = global_ac.get(alt, 0) + ac[alt] - global_dp += dp - - variant.INFO["{}_af".format(prefix)] = ",".join([str(self._calculate_af(global_ac[alt], global_dp)) for alt in variant.ALT]) - variant.INFO["{}_ac".format(prefix)] = ",".join([str(global_ac[alt]) for alt in variant.ALT]) - variant.INFO["{}_dp".format(prefix)] = global_dp - - def _add_insertion_stats(self, bams: List[AlignmentFile], variant: Variant, prefix: str): - - global_dp = 0 - global_ac = 0 - vafator_variant = build_variant(variant) - for i, b in enumerate(bams): - pileups = get_variant_pileup(variant=vafator_variant, bam=b, - min_base_quality=self.base_call_quality_threshold, - min_mapping_quality=self.mapping_quality_threshold) - ac, dp = get_insertion_metrics(variant=vafator_variant, pileups=pileups) - af = self._calculate_af(ac, dp) - if len(bams) > 1: - variant.INFO["{}_af_{}".format(prefix, i+1)] = af - variant.INFO["{}_ac_{}".format(prefix, i+1)] = ac - variant.INFO["{}_dp_{}".format(prefix, i+1)] = dp - global_ac += ac - global_dp += dp - - global_af = self._calculate_af(global_ac, global_dp) - variant.INFO["{}_af".format(prefix)] = global_af - variant.INFO["{}_ac".format(prefix)] = global_ac - variant.INFO["{}_dp".format(prefix)] = global_dp - - def _add_deletion_stats(self, bams: List[AlignmentFile], variant: Variant, prefix: str): - - global_dp = 0 - global_ac = 0 - vafator_variant = build_variant(variant) - for i, b in enumerate(bams): - pileups = get_variant_pileup(variant=vafator_variant, bam=b, - min_base_quality=self.base_call_quality_threshold, - min_mapping_quality=self.mapping_quality_threshold) - ac, dp = get_deletion_metrics(variant=vafator_variant, pileups=pileups) - af = self._calculate_af(ac, dp) - if len(bams) > 1: - variant.INFO["{}_af_{}".format(prefix, i+1)] = af - variant.INFO["{}_ac_{}".format(prefix, i+1)] = ac - variant.INFO["{}_dp_{}".format(prefix, i+1)] = dp - global_ac += ac - global_dp += dp - global_af = self._calculate_af(global_ac, global_dp) - variant.INFO["{}_af".format(prefix)] = global_af - variant.INFO["{}_ac".format(prefix)] = global_ac - variant.INFO["{}_dp".format(prefix)] = global_dp + for sample, bams in self.bam_readers.items(): + for i, bam in enumerate(bams): + pileups = get_variant_pileup( + variant=vafator_variant, bam=bam, + min_base_quality=self.base_call_quality_threshold, + min_mapping_quality=self.mapping_quality_threshold) + coverage_metrics = get_metrics(variant=vafator_variant, pileups=pileups) + if coverage_metrics is not None: + if len(bams) > 1: + variant.INFO["{}_af_{}".format(sample, i + 1)] = ",".join( + [str(self._calculate_af(coverage_metrics.ac[alt], coverage_metrics.dp)) for alt in variant.ALT]) + variant.INFO["{}_ac_{}".format(sample, i + 1)] = ",".join([str(coverage_metrics.ac[alt]) for alt in variant.ALT]) + variant.INFO["{}_dp_{}".format(sample, i + 1)] = coverage_metrics.dp + for alt in variant.ALT: + global_ac[alt] = global_ac.get(alt, 0) + coverage_metrics.ac[alt] + global_dp += coverage_metrics.dp + + variant.INFO["{}_af".format(sample)] = ",".join([str(self._calculate_af(global_ac[alt], global_dp)) for alt in variant.ALT]) + variant.INFO["{}_ac".format(sample)] = ",".join([str(global_ac[alt]) for alt in variant.ALT]) + variant.INFO["{}_dp".format(sample)] = global_dp def _calculate_af(self, ac, dp): return float(ac) / dp if dp > 0 else 0.0 @@ -155,20 +112,8 @@ def run(self): variant: Variant for variant in self.vcf: # gets the counts of all bases across all BAMs - if self.tumor_bams: - if variant.is_snp: - self._add_snv_stats(self.tumor_bams, variant, self.tumor_prefix) - elif variant.is_indel and not variant.is_deletion: - self._add_insertion_stats(self.tumor_bams, variant, self.tumor_prefix) - elif variant.is_indel and variant.is_deletion: - self._add_deletion_stats(self.tumor_bams, variant, self.tumor_prefix) - if self.normal_bams: - if variant.is_snp: - self._add_snv_stats(self.normal_bams, variant, self.normal_prefix) - elif variant.is_indel and not variant.is_deletion: - self._add_insertion_stats(self.normal_bams, variant, self.normal_prefix) - elif variant.is_indel and variant.is_deletion: - self._add_deletion_stats(self.normal_bams, variant, self.normal_prefix) + self._add_stats(variant) + batch.append(variant) if len(batch) >= 1000: self._write_batch(batch) @@ -178,5 +123,6 @@ def run(self): self.vcf_writer.close() self.vcf.close() - for b in self.tumor_bams + self.normal_bams: - b.close() + for _, bams in self.bam_readers.items(): + for bam in bams: + bam.close() diff --git a/vafator/command_line.py b/vafator/command_line.py index a1765c7..588e2a7 100755 --- a/vafator/command_line.py +++ b/vafator/command_line.py @@ -18,6 +18,11 @@ def annotator(): epilog=epilog) parser.add_argument("--input-vcf", dest="input_vcf", action="store", help="The VCF to annotate", required=True) parser.add_argument("--output-vcf", dest="output_vcf", action="store", help="The annotated VCF", required=True) + parser.add_argument('--bam', action='append', nargs=2, + metavar=('sample_name', 'bam_file'), + help='A sample name and a BAM file. Can be used multiple times to input multiple samples and ' + 'multiple BAM files. The same sample name can be used multiple times with different BAMs, ' + 'this will treated as replicates.') parser.add_argument("--normal-bams", dest="normal_bams", nargs='+', action="store", default=[], help="Whitespace-separated list of normal BAMs to analyse") parser.add_argument("--tumor-bams", dest="tumor_bams", nargs='+', action="store", default=[], @@ -26,22 +31,38 @@ def annotator(): help="All reads with a mapping quality below this threshold will be filtered out") parser.add_argument("--base-call-quality", dest="base_call_quality", action="store", type=int, default=30, help="All bases with a base call quality below this threshold will be filtered out") - parser.add_argument("--prefix", dest="prefix", action="store", type=str, default=None, - help="When provided the annotations are preceded by this prefix, otherwise the annotations" - "are named as tumor_af, normal_af, tumor_ac, normal_ac, tumor_dp and normal_dp") args = parser.parse_args() logging.info("Vafator starting...") + + bams = {} + for sample_name, bam in args.bam: + if sample_name in bams: + bams[sample_name].append(bam) + else: + bams[sample_name] = [bam] + for bam in args.tumor_bams: + if "tumor" in bams: + bams["tumor"].append(bam) + else: + bams["tumor"] = [bam] + for bam in args.normal_bams: + if "normal" in bams: + bams["normal"].append(bam) + else: + bams["normal"] = [bam] + + if len(bams) == 0: + raise ValueError("Please, provide at least one bam file through either --bam, --tumor-bams or --normal-bams") + try: annotator = Annotator( input_vcf=args.input_vcf, output_vcf=args.output_vcf, - normal_bams=args.normal_bams, - tumor_bams=args.tumor_bams, + input_bams=bams, mapping_qual_thr=args.mapping_quality, - base_call_qual_thr=args.base_call_quality, - prefix=args.prefix + base_call_qual_thr=args.base_call_quality ) annotator.run() except Exception as e: diff --git a/vafator/pileups.py b/vafator/pileups.py index 7534c13..953a098 100644 --- a/vafator/pileups.py +++ b/vafator/pileups.py @@ -11,6 +11,15 @@ class VafatorVariant: reference: str alternative: List[str] + def is_snp(self): + return len(self.reference) == 1 and len(self.alternative[0]) == 1 + + def is_insertion(self): + return len(self.reference) == 1 and len(self.alternative[0]) > 1 + + def is_deletion(self): + return len(self.alternative[0]) == 1 and len(self.reference) > 1 + def build_variant(variant: Variant) -> VafatorVariant: return VafatorVariant( @@ -32,8 +41,24 @@ def get_variant_pileup( min_mapping_quality=min_mapping_quality) -def get_insertion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion): - ac = 0 +@dataclass +class CoverageMetrics: + ac: dict + dp: int + + +def get_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion) -> CoverageMetrics: + if variant.is_snp(): + return get_snv_metrics(variant, pileups) + elif variant.is_insertion(): + return get_insertion_metrics(variant, pileups) + elif variant.is_deletion(): + return get_deletion_metrics(variant, pileups) + return None + + +def get_insertion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion) -> CoverageMetrics: + ac = {alt.upper(): 0 for alt in variant.alternative} dp = 0 position = variant.position insertion_length = len(variant.alternative[0]) - len(variant.reference) @@ -57,15 +82,15 @@ def get_insertion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion insertion_in_query = r.alignment.query[relative_position:relative_position + insertion_length] if start == position and cigar_length == insertion_length and \ insertion == insertion_in_query: - ac += 1 + ac[variant.alternative[0].upper()] = ac[variant.alternative[0].upper()] + 1 except StopIteration: # no reads pass - return ac, dp + return CoverageMetrics(ac=ac, dp=dp) -def get_deletion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion): - ac = 0 +def get_deletion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion) -> CoverageMetrics: + ac = {alt.upper(): 0 for alt in variant.alternative} dp = 0 position = variant.position deletion_length = len(variant.reference) - len(variant.alternative[0]) @@ -81,7 +106,7 @@ def get_deletion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion) start += cigar_length elif cigar_type == 2: # D if start == position and cigar_length == deletion_length: - ac += 1 + ac[variant.alternative[0].upper()] = ac[variant.alternative[0].upper()] + 1 else: start += cigar_length if start > position: @@ -89,7 +114,7 @@ def get_deletion_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion) except StopIteration: # no reads pass - return ac, dp + return CoverageMetrics(ac=ac, dp=dp) def _initialize_empty_count(bases_counts, base): @@ -98,7 +123,7 @@ def _initialize_empty_count(bases_counts, base): return bases_counts -def get_snv_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion): +def get_snv_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion) -> CoverageMetrics: dp = 0 ac = {alt.upper(): 0 for alt in variant.alternative} ac[variant.reference.upper()] = 0 @@ -112,4 +137,4 @@ def get_snv_metrics(variant: VafatorVariant, pileups: IteratorColumnRegion): except StopIteration: # no reads pass - return ac, dp + return CoverageMetrics(ac=ac, dp=dp) diff --git a/vafator/tests/resources/results/project.NIST.hc.snps.indels.chr1_1000000_2000000.vaf.vcf b/vafator/tests/resources/results/project.NIST.hc.snps.indels.chr1_1000000_2000000.vaf.vcf index e833d8b..b2bc43f 100644 --- a/vafator/tests/resources/results/project.NIST.hc.snps.indels.chr1_1000000_2000000.vaf.vcf +++ b/vafator/tests/resources/results/project.NIST.hc.snps.indels.chr1_1000000_2000000.vaf.vcf @@ -121,10 +121,10 @@ ##reference=file:///share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.5/hg19/ucsc.hg19.fasta ##bcftools_filterVersion=1.10.2+htslib-1.10.2 ##bcftools_filterCommand=filter -r chr1:1000000-2000000 project.NIST.hc.snps.indels.vcf.gz; Date=Tue Nov 9 22:01:40 2021 -##vafator_command_line={"name": "vafator", "version": "1.0.0", "date": "Wed Nov 10 17:03:09 2021", "timestamp": 1636560189.413893, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/project.NIST.hc.snps.indels.chr1_1000000_2000000.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/project.NIST.hc.snps.indels.chr1_1000000_2000000.vaf.vcf", "normal_bams": ["/home/priesgo/src/github/vafator/vafator/tests/resources/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.chr1_1000000_2000000.bam"], "tumor_bams": [], "mapping_quality_threshold": 0, "base_call_quality_threshold": 29, "prefix": null} -##INFO= -##INFO= -##INFO= +##vafator_command_line={"name": "vafator", "version": "1.0.0", "date": "Wed Nov 10 22:30:59 2021", "timestamp": 1636579859.455694, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/project.NIST.hc.snps.indels.chr1_1000000_2000000.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/project.NIST.hc.snps.indels.chr1_1000000_2000000.vaf.vcf", "bams": "normal:/home/priesgo/src/github/vafator/vafator/tests/resources/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.chr1_1000000_2000000.bam", "mapping_quality_threshold": 0, "base_call_quality_threshold": 29} +##INFO= +##INFO= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NIST7035 NIST7086 chr1 1001177 rs4970401 G C 141.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=2.637;ClippingRankSum=-1.749;DB;DP=11;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.466;QD=12.86;ReadPosRankSum=1.186;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 0/1:2,1:3:32:32,0,69 0/1:4,4:8:99:138,0,104 chr1 1017170 rs3766193 C G 273.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.2;ClippingRankSum=-0.933;DB;DP=14;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.8;QD=19.53;ReadPosRankSum=0.267;normal_af=0.5;normal_ac=1;normal_dp=2 GT:AD:DP:GQ:PL 0/1:3,3:6:95:100,0,95 0/1:2,6:8:56:202,0,56 @@ -136,17 +136,17 @@ chr1 1023444 rs9442399 C G 60.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF= chr1 1026801 rs4562563 T A 1354.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.853;ClippingRankSum=-1.696;DB;DP=66;FS=0;MLEAC=2;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=-2.019;QD=20.52;ReadPosRankSum=1.373;normal_af=0.6;normal_ac=9;normal_dp=15 GT:AD:DP:GQ:PL 0/1:13,18:31:99:576,0,397 0/1:10,25:35:99:807,0,269 chr1 1060355 rs12567855 G C 61.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=20.57;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 ./.:.:.:.:. chr1 1064670 rs7547403 C G 85.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=21.37;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,4:4:12:112,12,0 -chr1 1066388 rs140634183 C CT 77.8 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=25.93;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 1/1:0,2:2:6:75,6,0 -chr1 1067674 rs35574593 T TGG 190.31 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=55.21;MQ0=0;QD=19.03;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,4:4:12:180,12,0 +chr1 1066388 rs140634183 C CT 77.8 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=25.93;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 1/1:0,2:2:6:75,6,0 +chr1 1067674 rs35574593 T TGG 190.31 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=55.21;MQ0=0;QD=19.03;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,4:4:12:180,12,0 chr1 1067862 rs9442374 T G 109.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=29.41;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 1/1:0,1:1:3:45,3,0 chr1 1067865 rs9442358 A C 109.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=24.66;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 1/1:0,1:1:3:45,3,0 -chr1 1068832 rs146603024 CGCCGCCTGCCTGCCCG C 55.95 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=34.37;MQ0=0;QD=1.75;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:7:91,7,0 +chr1 1068832 rs146603024 CGCCGCCTGCCTGCCCG C 55.95 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=34.37;MQ0=0;QD=1.75;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:7:91,7,0 chr1 1070128 rs9442378 T G 60.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=20.28;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 1/1:0,2:2:6:49,6,0 chr1 1071118 rs10907183 G C 72.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=49.84;MQ0=0;QD=18.12;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 ./.:.:.:.:. chr1 1077962 rs55750860 C T 94.31 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=49.84;MQ0=0;QD=23.58;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,2:2:6:71,6,0 chr1 1098421 rs12135382 C T 63.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=21.28;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:49,6,0 chr1 1103542 rs7518873 T C 165.35 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=33.07;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 1/1:0,4:4:12:153,12,0 -chr1 1113941 . CAA C 31.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=7.78;normal_af=1;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 ./.:.:.:.:. +chr1 1113941 . CAA C 31.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=7.78;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 ./.:.:.:.:. chr1 1132760 . A C 50.57 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.727;ClippingRankSum=-0.727;DP=4;FS=6.021;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.727;QD=12.64;ReadPosRankSum=-0.727;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 0/1:1,1:2:4:4,0,57 0/1:0,2:2:58:74,0,58 chr1 1132766 . T C 50.57 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.231;ClippingRankSum=-1.231;DP=5;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.358;QD=10.11;ReadPosRankSum=-1.231;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:1,0:1:4:4,0,57 0/1:2,2:4:58:74,0,58 chr1 1149661 rs35878953 C T 221.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=2.475;ClippingRankSum=0.386;DB;DP=14;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.865;QD=15.82;ReadPosRankSum=-0.386;normal_af=1.0;normal_ac=5;normal_dp=5 GT:AD:DP:GQ:PL 0/1:2,5:7:48:162,0,48 0/1:4,3:7:88:88,0,120 @@ -158,9 +158,9 @@ chr1 1159182 . G C 355.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.291;ClippingRank chr1 1159187 . A C 355.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.147;ClippingRankSum=-0.317;DP=29;FS=26.578;MLEAC=2;MLEAF=0.5;MQ=52.38;MQ0=0;MQRankSum=-2.562;QD=12.26;ReadPosRankSum=-1.195;normal_af=0.0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/1:6,2:8:99:99,0,635 0/1:15,6:21:99:285,0,1644 chr1 1159191 . A C 355.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.501;ClippingRankSum=0.326;DP=32;FS=8.907;MLEAC=2;MLEAF=0.5;MQ=52.48;MQ0=0;MQRankSum=-2.198;QD=11.11;ReadPosRankSum=-2.198;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 0/1:8,1:9:99:99,0,635 0/1:16,7:23:99:285,0,1644 chr1 1159517 rs6702268 T C 365.35 PASS AC=4;AF=1;AN=4;DB;DP=11;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=33.21;normal_af=1.0;normal_ac=5;normal_dp=5 GT:AD:DP:GQ:PL 1/1:0,7:7:21:252,21,0 1/1:0,4:4:12:140,12,0 -chr1 1186736 rs58561267 AT A 32.81 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=10.94;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:22,3,0 1/1:0,2:2:6:45,6,0 +chr1 1186736 rs58561267 AT A 32.81 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=10.94;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:22,3,0 1/1:0,2:2:6:45,6,0 chr1 1196863 rs6659787 T C 3222.27 PASS AC=4;AF=1;AN=4;DB;DP=102;FS=0;MLEAC=4;MLEAF=1;MQ=57.01;MQ0=0;QD=31.59;normal_af=1.0;normal_ac=14;normal_dp=14 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1406,132,0 1/1:0,58:58:99:1843,174,0 -chr1 1221345 . GCAC G 39.24 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=1.271;ClippingRankSum=0.898;DP=10;FS=0;MLEAC=1;MLEAF=0.25;MQ=53.27;MQ0=0;MQRankSum=1.271;QD=3.27;ReadPosRankSum=-1.495;normal_af=0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,84 0/0:6,0:6:18:0,18,227 +chr1 1221345 . GCAC G 39.24 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=1.271;ClippingRankSum=0.898;DP=10;FS=0;MLEAC=1;MLEAF=0.25;MQ=53.27;MQ0=0;MQRankSum=1.271;QD=3.27;ReadPosRankSum=-1.495;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,84 0/0:6,0:6:18:0,18,227 chr1 1222690 rs115316182 C T 662.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=2.694;ClippingRankSum=1.528;DB;DP=61;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.465;QD=10.86;ReadPosRankSum=0.436;normal_af=0.5333333333333333;normal_ac=8;normal_dp=15 GT:AD:DP:GQ:PL 0/1:21,15:36:99:433,0,584 0/1:16,9:25:99:258,0,484 chr1 1224131 . T C 100.59 PASS AC=4;AF=1;AN=4;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=36.51;MQ0=0;QD=25.15;normal_af=0.5;normal_ac=2;normal_dp=4 GT:AD:DP:GQ:PL 1/1:0,3:3:9:116,9,0 1/1:0,1:1:3:10,3,0 chr1 1229680 rs2477781 G T 384.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.997;ClippingRankSum=2.005;DB;DP=31;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-2.084;QD=12.4;ReadPosRankSum=0.179;normal_af=0.5714285714285714;normal_ac=4;normal_dp=7 GT:AD:DP:GQ:PL 0/1:7,7:14:99:213,0,222 0/1:10,7:17:99:200,0,328 @@ -168,7 +168,7 @@ chr1 1239339 rs11260584 T G 325.37 PASS AC=4;AF=1;AN=4;DB;DP=10;FS=0;MLEAC=4;MLE chr1 1245368 rs11590283 G A 227.21 PASS AC=4;AF=1;AN=4;DB;DP=7;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=32.46;normal_af=1.0;normal_ac=4;normal_dp=4 GT:AD:DP:GQ:PL 1/1:0,6:6:18:215,18,0 1/1:0,1:1:3:38,3,0 chr1 1246004 rs2296474 A G 3320.2 PASS AC=4;AF=1;AN=4;DB;DP=112;FS=0;MLEAC=4;MLEAF=1;MQ=58.79;MQ0=0;QD=29.64;normal_af=1.0;normal_ac=20;normal_dp=20 GT:AD:DP:GQ:PL 1/1:0,56:56:99:1722,168,0 1/1:0,56:56:99:1625,168,0 chr1 1247494 rs12103 T C 3691.2 PASS AC=4;AF=1;AN=4;DB;DP=124;FS=0;MLEAC=4;MLEAF=1;MQ=54.92;MQ0=0;QD=29.77;normal_af=1.0;normal_ac=21;normal_dp=21 GT:AD:DP:GQ:PL 1/1:0,64:64:99:1914,192,0 1/1:0,59:59:99:1804,177,0 -chr1 1247578 . T TGG 155.42 PASS AC=2;AF=0.5;AN=4;DP=14;FS=0;MLEAC=2;MLEAF=0.5;MQ=60.89;MQ0=0;QD=5.55;normal_af=0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/1:0,4:4:0:94,0,0 0/1:0,7:7:38:141,0,38 +chr1 1247578 . T TGG 155.42 PASS AC=2;AF=0.5;AN=4;DP=14;FS=0;MLEAC=2;MLEAF=0.5;MQ=60.89;MQ0=0;QD=5.55;normal_af=0.0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/1:0,4:4:0:94,0,0 0/1:0,7:7:38:141,0,38 chr1 1249187 rs12142199 G A 4740.2 PASS AC=4;AF=1;AN=4;DB;DP=160;FS=0;MLEAC=4;MLEAF=1;MQ=58.35;MQ0=0;QD=29.63;normal_af=1.0;normal_ac=23;normal_dp=23 GT:AD:DP:GQ:PL 1/1:0,91:91:99:2678,273,0 1/1:0,69:69:99:2089,207,0 chr1 1254841 rs10907179 C G 3506.2 PASS AC=4;AF=1;AN=4;DB;DP=103;FS=0;MLEAC=4;MLEAF=1;MQ=58.54;MQ0=0;QD=34.04;normal_af=1.0;normal_ac=20;normal_dp=20 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1826,159,0 1/1:0,50:50:99:1707,150,0 chr1 1260168 rs61766199 C A 421.61 PASS AC=4;AF=1;AN=4;DB;DP=14;FS=0;MLEAC=4;MLEAF=1;MQ=58.33;MQ0=0;QD=30.12;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:7:100,7,0 1/1:0,11:11:31:348,31,0 @@ -187,10 +187,10 @@ chr1 1273278 rs307370 A G 747.21 PASS AC=4;AF=1;AN=4;DB;DP=20;FS=0;MLEAC=4;MLEAF chr1 1273614 . T C 431.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.19;ClippingRankSum=-1.948;DP=44;FS=35.789;MLEAC=2;MLEAF=0.5;MQ=59.45;MQ0=0;MQRankSum=0.301;QD=9.81;ReadPosRankSum=0.614;normal_af=0.3333333333333333;normal_ac=1;normal_dp=3 GT:AD:DP:GQ:PL 0/1:10,10:20:99:248,0,617 0/1:9,12:21:99:212,0,728 chr1 1273622 . G C 431.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.049;ClippingRankSum=-4.155;DP=52;FS=23.478;MLEAC=2;MLEAF=0.5;MQ=58.81;MQ0=0;MQRankSum=0.759;QD=8.3;ReadPosRankSum=-2.593;normal_af=0.125;normal_ac=1;normal_dp=8 GT:AD:DP:GQ:PL 0/1:14,6:20:99:248,0,617 0/1:22,7:29:99:212,0,728 chr1 1274242 rs307369 A G 62.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=45.96;MQ0=0;QD=20.9;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:89,9,0 -chr1 1275264 rs59153307 A ACAGCCGCATGTCCCCCAGCAGCCCCCACAGACCCACCCG 552.64 PASS AC=2;AF=0.5;AN=4;DB;DP=42;FS=0;MLEAC=2;MLEAF=0.5;MQ=59.45;MQ0=0;QD=0.34;normal_af=0;normal_ac=0;normal_dp=10 GT:AD:DP:GQ:PL 0/1:0,8:8:3:294,0,3 0/1:0,11:11:7:294,0,7 +chr1 1275264 rs59153307 A ACAGCCGCATGTCCCCCAGCAGCCCCCACAGACCCACCCG 552.64 PASS AC=2;AF=0.5;AN=4;DB;DP=42;FS=0;MLEAC=2;MLEAF=0.5;MQ=59.45;MQ0=0;QD=0.34;normal_af=0.0;normal_ac=0;normal_dp=10 GT:AD:DP:GQ:PL 0/1:0,8:8:3:294,0,3 0/1:0,11:11:7:294,0,7 chr1 1276459 rs307365 C A 64.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=32.08;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:90,6,0 chr1 1276478 rs307364 T G 64.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=32.08;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:90,6,0 -chr1 1276973 rs145370195 G GACAC 672.2 PASS AC=4;AF=1;AN=4;DB;DP=13;FS=0;MLEAC=4;MLEAF=1;MQ=44.08;MQ0=0;QD=12.93;normal_af=0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,5:5:18:286,18,0 1/1:0,8:8:27:422,27,0 +chr1 1276973 rs145370195 G GACAC 672.2 PASS AC=4;AF=1;AN=4;DB;DP=13;FS=0;MLEAC=4;MLEAF=1;MQ=44.08;MQ0=0;QD=12.93;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,5:5:18:286,18,0 1/1:0,8:8:27:422,27,0 chr1 1277533 rs307362 T C 7596.2 PASS AC=4;AF=1;AN=4;DB;DP=257;FS=0;MLEAC=4;MLEAF=1;MQ=56.57;MQ0=0;QD=29.56;normal_af=1.0;normal_ac=42;normal_dp=42 GT:AD:DP:GQ:PL 1/1:0,130:130:99:3918,390,0 1/1:0,127:127:99:3705,381,0 chr1 1278237 rs307361 T C 1087.2 PASS AC=4;AF=1;AN=4;DB;DP=31;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=30.26;normal_af=1.0;normal_ac=8;normal_dp=8 GT:AD:DP:GQ:PL 1/1:0,13:13:39:464,39,0 1/1:0,18:18:54:650,54,0 chr1 1279025 rs307360 A G 72.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=49.84;MQ0=0;QD=18.12;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 ./.:.:.:.:. @@ -200,25 +200,25 @@ chr1 1288345 rs13249 A G 6789.2 PASS AC=4;AF=1;AN=4;DB;DP=198;FS=0;MLEAC=4;MLEAF chr1 1288471 rs3766183 C T 3765.2 PASS AC=4;AF=1;AN=4;DB;DP=115;FS=0;MLEAC=4;MLEAF=1;MQ=58.03;MQ0=0;QD=32.74;normal_af=1.0;normal_ac=24;normal_dp=24 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1657,141,0 1/1:0,66:66:99:2135,198,0 chr1 1288583 rs3845295 C G 2200.2 PASS AC=4;AF=1;AN=4;DB;DP=62;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=31.61;normal_af=1.0;normal_ac=17;normal_dp=17 GT:AD:DP:GQ:PL 1/1:0,30:30:90:1086,90,0 1/1:0,32:32:96:1141,96,0 chr1 1288823 rs2296471 A G 2505.2 PASS AC=4;AF=1;AN=4;DB;DP=68;FS=0;MLEAC=4;MLEAF=1;MQ=59.72;MQ0=0;QD=28.68;normal_af=1.0;normal_ac=16;normal_dp=16 GT:AD:DP:GQ:PL 1/1:0,32:32:96:1191,96,0 1/1:0,36:36:99:1341,108,0 -chr1 1289367 rs140777846 CTG C 10734.2 PASS AC=4;AF=1;AN=4;DB;DP=252;FS=0;MLEAC=4;MLEAF=1;MQ=59.47;MQ0=0;QD=21.3;normal_af=0.956522;normal_ac=44;normal_dp=46 GT:AD:DP:GQ:PL 1/1:0,115:115:99:5040,357,0 1/1:0,129:129:99:5730,399,0 +chr1 1289367 rs140777846 CTG C 10734.2 PASS AC=4;AF=1;AN=4;DB;DP=252;FS=0;MLEAC=4;MLEAF=1;MQ=59.47;MQ0=0;QD=21.3;normal_af=0.9565217391304348;normal_ac=44;normal_dp=46 GT:AD:DP:GQ:PL 1/1:0,115:115:99:5040,357,0 1/1:0,129:129:99:5730,399,0 chr1 1289911 rs4970365 G A 2670.2 PASS AC=4;AF=1;AN=4;BaseQRankSum=1.597;ClippingRankSum=1.057;DB;DP=77;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.012;QD=34.68;ReadPosRankSum=0.787;normal_af=1.0;normal_ac=15;normal_dp=15 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1201,99,0 1/1:1,43:44:99:1496,121,0 chr1 1290276 rs75904949 C G 1563.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.205;ClippingRankSum=-0.499;DB;DP=120;FS=4.648;MLEAC=2;MLEAF=0.5;MQ=59.53;MQ0=0;MQRankSum=0.787;QD=13.03;ReadPosRankSum=1.286;normal_af=0.47619047619047616;normal_ac=10;normal_dp=21 GT:AD:DP:GQ:PL 0/1:27,27:54:99:715,0,704 0/1:34,32:66:99:877,0,1036 chr1 1291159 rs201260508 GA G 814.16 PASS AC=4;AF=1;AN=4;DB;DP=26;FS=0;MLEAC=4;MLEAF=1;MQ=59.61;MQ0=0;QD=31.31;normal_af=0.25;normal_ac=1;normal_dp=4 GT:AD:DP:GQ:PL 1/1:0,12:12:37:418,37,0 1/1:0,12:12:37:432,37,0 chr1 1292426 rs35694341 C G 52.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=26.08;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:78,6,0 chr1 1293764 rs34841888 G C 1190.2 PASS AC=4;AF=1;AN=4;DB;DP=33;FS=0;MLEAC=4;MLEAF=1;MQ=58.86;MQ0=0;QD=30.18;normal_af=1.0;normal_ac=8;normal_dp=8 GT:AD:DP:GQ:PL 1/1:0,13:13:39:490,39,0 1/1:0,20:20:60:727,60,0 -chr1 1296369 rs138096037 GAC G 54.13 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=65.19;MQ0=0;QD=13.53;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:89,6,0 +chr1 1296369 rs138096037 GAC G 54.13 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=65.19;MQ0=0;QD=13.53;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:89,6,0 chr1 1296818 rs2765024 C G 55.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=27.58;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:81,6,0 -chr1 1302326 . GAAT G 52.13 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0;MLEAC=2;MLEAF=0.5;MQ=45.96;MQ0=0;MQRankSum=-0.736;QD=8.69;ReadPosRankSum=0.736;normal_af=0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 0/0:1,0:1:3:0,3,70 +chr1 1302326 . GAAT G 52.13 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0;MLEAC=2;MLEAF=0.5;MQ=45.96;MQ0=0;MQRankSum=-0.736;QD=8.69;ReadPosRankSum=0.736;normal_af=0.0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 0/0:1,0:1:3:0,3,70 chr1 1302330 . G C 61.17 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0;MLEAC=2;MLEAF=0.5;MQ=45.96;MQ0=0;MQRankSum=-0.736;QD=30.58;ReadPosRankSum=-0.736;normal_af=0.0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 0/0:1,0:1:3:0,3,70 chr1 1302408 rs61766242 A G 72.31 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=18.08;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,2:2:6:49,6,0 -chr1 1305933 . CAAAA C 55.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=65.19;MQ0=0;QD=6.89;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:90,6,0 +chr1 1305933 . CAAAA C 55.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=65.19;MQ0=0;QD=6.89;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:90,6,0 chr1 1308871 rs2649595 A T 95.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=23.87;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,4:4:12:122,12,0 chr1 1308982 rs2765015 A G 947.2 PASS AC=4;AF=1;AN=4;DB;DP=27;FS=0;MLEAC=4;MLEAF=1;MQ=59.14;MQ0=0;QD=27.91;normal_af=1.0;normal_ac=4;normal_dp=4 GT:AD:DP:GQ:PL 1/1:0,11:11:33:387,33,0 1/1:0,16:16:48:587,48,0 chr1 1310074 rs2765035 C G 9981.2 PASS AC=4;AF=1;AN=4;DB;DP=337;FS=0;MLEAC=4;MLEAF=1;MQ=57.41;MQ0=0;QD=29.62;normal_af=1.0;normal_ac=32;normal_dp=32 GT:AD:DP:GQ:PL 1/1:0,125:125:99:3745,375,0 1/1:0,212:212:99:6263,636,0 chr1 1310668 rs2242398 A C 2775.2 PASS AC=4;AF=1;AN=4;DB;DP=76;FS=0;MLEAC=4;MLEAF=1;MQ=59.51;MQ0=0;QD=29.79;normal_af=1.0;normal_ac=17;normal_dp=17 GT:AD:DP:GQ:PL 1/1:0,39:39:99:1427,117,0 1/1:0,37:37:99:1375,111,0 chr1 1310924 rs2765033 T C 620.21 PASS AC=4;AF=1;AN=4;DB;DP=18;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=34.46;normal_af=1.0;normal_ac=7;normal_dp=7 GT:AD:DP:GQ:PL 1/1:0,8:8:24:288,24,0 1/1:0,10:10:30:359,30,0 chr1 1310975 rs2649594 C T 293.4 PASS AC=4;AF=1;AN=4;DB;DP=9;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=32.6;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,5:5:15:177,15,0 1/1:0,4:4:12:143,12,0 -chr1 1314463 . AT A 185.32 PASS AC=4;AF=1;AN=4;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=52.03;MQ0=0;QD=27.95;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,4:4:12:180,12,0 +chr1 1314463 . AT A 185.32 PASS AC=4;AF=1;AN=4;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=52.03;MQ0=0;QD=27.95;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,4:4:12:180,12,0 chr1 1314471 rs2313135 T G 189.32 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=52.03;MQ0=0;QD=30.09;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,4:4:12:180,12,0 chr1 1314707 rs2260423 A G 64.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=32.08;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 ./.:.:.:.:. chr1 1314714 rs2260424 A G 64.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=32.08;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 ./.:.:.:.:. @@ -228,7 +228,7 @@ chr1 1316670 rs2765029 C G 112.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF chr1 1316674 rs2649585 C T 112.46 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=33.61;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:12:139,12,0 ./.:.:.:.:. chr1 1320764 rs4970444 G A 55.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=18.61;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,1:1:3:32,3,0 chr1 1323078 rs12729599 A G 711.21 PASS AC=4;AF=1;AN=4;DB;DP=21;FS=0;MLEAC=4;MLEAF=1;MQ=58.2;MQ0=0;QD=33.87;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,7:7:21:233,21,0 1/1:0,14:14:42:505,42,0 -chr1 1323143 rs141100746 CCT C 5201.16 PASS AC=4;AF=1;AN=4;DB;DP=118;FS=0;MLEAC=4;MLEAF=1;MQ=58.5;MQ0=0;QD=22.04;normal_af=0.952381;normal_ac=20;normal_dp=21 GT:AD:DP:GQ:PL 1/1:0,57:57:99:2555,177,0 1/1:0,61:61:99:2682,189,0 +chr1 1323143 rs141100746 CCT C 5201.16 PASS AC=4;AF=1;AN=4;DB;DP=118;FS=0;MLEAC=4;MLEAF=1;MQ=58.5;MQ0=0;QD=22.04;normal_af=0.9523809523809523;normal_ac=20;normal_dp=21 GT:AD:DP:GQ:PL 1/1:0,57:57:99:2555,177,0 1/1:0,61:61:99:2682,189,0 chr1 1342612 rs2275915 G C 501.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.815;ClippingRankSum=0.957;DB;DP=34;FS=5.294;MLEAC=2;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=0.035;QD=14.75;ReadPosRankSum=-0.567;normal_af=0.6666666666666666;normal_ac=2;normal_dp=3 GT:AD:DP:GQ:PL 0/1:4,13:17:72:308,0,72 0/1:9,8:17:99:222,0,227 chr1 1365334 rs1781138 A G 95.52 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=23.88;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 1/1:0,3:3:9:84,9,0 chr1 1366600 . C A 72.46 PASS AC=2;AF=1;AN=2;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=18.12;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 ./.:.:.:.:. @@ -238,7 +238,7 @@ chr1 1414225 . G T 42.17 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=29;MQ0 chr1 1417696 rs819970 C G 378.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.463;ClippingRankSum=-1.812;DB;DP=60;FS=1.886;MLEAC=2;MLEAF=0.5;MQ=50.88;MQ0=0;MQRankSum=-5.578;QD=6.31;ReadPosRankSum=1.065;normal_af=0.375;normal_ac=6;normal_dp=16 GT:AD:DP:GQ:PL 0/1:21,12:33:99:262,0,675 0/1:20,7:27:99:145,0,692 chr1 1420637 rs35871802 C T 168.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.369;ClippingRankSum=-0.811;DB;DP=13;FS=0;MLEAC=2;MLEAF=0.5;MQ=49.42;MQ0=0;MQRankSum=-1.369;QD=12.96;ReadPosRankSum=0.101;normal_af=0.0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/1:2,1:3:28:28,0,65 0/1:4,6:10:99:169,0,120 chr1 1423281 rs79849353 G A 3799.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.404;ClippingRankSum=0.848;DB;DP=341;FS=1.307;MLEAC=2;MLEAF=0.5;MQ=56.07;MQ0=0;MQRankSum=-0.188;QD=11.14;ReadPosRankSum=0.898;normal_af=0.4423076923076923;normal_ac=23;normal_dp=52 GT:AD:DP:GQ:PL 0/1:93,79:172:99:1926,0,2214 0/1:90,79:169:99:1902,0,2191 -chr1 1444869 . C CG 334.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.469;ClippingRankSum=-5.673;DP=108;FS=92.223;MLEAC=2;MLEAF=0.5;MQ=55.03;MQ0=0;MQRankSum=4.154;QD=3.1;ReadPosRankSum=-1.057;normal_af=0;normal_ac=0;normal_dp=18 GT:AD:DP:GQ:PL 0/1:27,10:37:99:140,0,716 0/1:31,15:46:99:232,0,769 +chr1 1444869 . C CG 334.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.469;ClippingRankSum=-5.673;DP=108;FS=92.223;MLEAC=2;MLEAF=0.5;MQ=55.03;MQ0=0;MQRankSum=4.154;QD=3.1;ReadPosRankSum=-1.057;normal_af=0.0;normal_ac=0;normal_dp=18 GT:AD:DP:GQ:PL 0/1:27,10:37:99:140,0,716 0/1:31,15:46:99:232,0,769 chr1 1458073 rs3118507 A G 865.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=6.258;ClippingRankSum=-0.044;DB;DP=54;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.62;MQ0=0;MQRankSum=-4.9;QD=16.03;ReadPosRankSum=1.349;normal_af=0.6153846153846154;normal_ac=8;normal_dp=13 GT:AD:DP:GQ:PL 0/1:12,15:27:99:453,0,347 0/1:12,15:27:99:441,0,351 chr1 1460355 . C A 35.2 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0;DP=4;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=1.026;QD=8.8;ReadPosRankSum=1.026;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 0/1:2,2:4:62:62,0,63 chr1 1469546 rs3128344 G A 2529.2 PASS AC=4;AF=1;AN=4;DB;DP=76;FS=0;MLEAC=4;MLEAF=1;MQ=54.62;MQ0=0;QD=33.28;normal_af=1.0;normal_ac=20;normal_dp=20 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1118,99,0 1/1:0,43:43:99:1438,129,0 @@ -246,21 +246,21 @@ chr1 1472234 . C A 42.17 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0 chr1 1474871 rs9439465 G C 133.44 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=0.198;ClippingRankSum=0.198;DB;DP=7;FS=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=0.922;QD=22.24;ReadPosRankSum=0.198;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,33 0/1:1,5:6:19:161,0,19 chr1 1491251 rs12048706 T C 57.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=19.24;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:84,9,0 chr1 1499298 rs9439468 A G 61.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=20.57;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:88,9,0 -chr1 1500485 rs141720989 CAAGGCAGGCGGATCATG C 103.47 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=39.12;MQ0=0;QD=1.52;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:7:91,7,0 1/1:0,1:1:4:47,4,0 +chr1 1500485 rs141720989 CAAGGCAGGCGGATCATG C 103.47 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=39.12;MQ0=0;QD=1.52;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:7:91,7,0 1/1:0,1:1:4:47,4,0 chr1 1500941 rs6603791 A G 63.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=21.28;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:49,6,0 chr1 1504560 rs7552586 T A 57.23 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.731;ClippingRankSum=0.731;DB;DP=5;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.731;QD=11.45;ReadPosRankSum=-0.731;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 0/1:1,4:5:21:84,0,21 chr1 1505674 rs34871297 CA C 32.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.922;ClippingRankSum=0.421;DB;DP=8;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.421;QD=4.05;ReadPosRankSum=-0.922;normal_af=0.5;normal_ac=1;normal_dp=2 GT:AD:DP:GQ:PL 0/1:2,2:4:37:37,0,45 0/1:2,2:4:33:33,0,44 -chr1 1505948 rs70949597 AC A 174.5 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.382;ClippingRankSum=0.382;DB;DP=13;FS=0;MLEAC=2;MLEAF=0.5;MQ=61.64;MQ0=0;MQRankSum=0.382;QD=13.42;ReadPosRankSum=0.566;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:1,4:5:15:107,0,15 0/1:2,4:6:41:105,0,41 +chr1 1505948 rs70949597 AC A 174.5 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.382;ClippingRankSum=0.382;DB;DP=13;FS=0;MLEAC=2;MLEAF=0.5;MQ=61.64;MQ0=0;MQRankSum=0.382;QD=13.42;ReadPosRankSum=0.566;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:1,4:5:15:107,0,15 0/1:2,4:6:41:105,0,41 chr1 1505967 rs7548959 C T 134.46 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.198;ClippingRankSum=-0.198;DB;DP=7;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.198;QD=19.21;ReadPosRankSum=-0.922;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 0/1:1,1:2:29:32,0,29 0/1:1,4:5:23:131,0,23 chr1 1506035 rs7540231 G A 473.24 PASS AC=4;AF=1;AN=4;DB;DP=15;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=31.55;normal_af=1.0;normal_ac=3;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,6:6:18:190,18,0 1/1:0,9:9:27:310,27,0 chr1 1509825 rs6666293 A G 1015.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.339;ClippingRankSum=-0.796;DB;DP=99;FS=1.668;MLEAC=2;MLEAF=0.5;MQ=58.67;MQ0=0;MQRankSum=-0.889;QD=10.26;ReadPosRankSum=-0.146;normal_af=0.65;normal_ac=13;normal_dp=20 GT:AD:DP:GQ:PL 0/1:28,24:52:99:601,0,730 0/1:26,20:46:99:443,0,709 -chr1 1510035 rs150737039 GGC G 1442.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.688;ClippingRankSum=1.356;DB;DP=59;FS=5.431;MLEAC=2;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=0.525;QD=12.22;ReadPosRankSum=-3.049;normal_af=0.909091;normal_ac=10;normal_dp=11 GT:AD:DP:GQ:PL 0/1:5,16:21:99:648,0,172 0/1:17,21:38:99:832,0,674 +chr1 1510035 rs150737039 GGC G 1442.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.688;ClippingRankSum=1.356;DB;DP=59;FS=5.431;MLEAC=2;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=0.525;QD=12.22;ReadPosRankSum=-3.049;normal_af=0.9090909090909091;normal_ac=10;normal_dp=11 GT:AD:DP:GQ:PL 0/1:5,16:21:99:648,0,172 0/1:17,21:38:99:832,0,674 chr1 1521805 rs4648786 A G 72.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=18.12;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 ./.:.:.:.:. chr1 1529457 rs28566709 T C 55.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=18.61;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:32,3,0 1/1:0,2:2:6:49,6,0 chr1 1529950 rs28503881 A G 67.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.72;ClippingRankSum=-0.72;DB;DP=6;FS=0;MLEAC=2;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=-0.72;QD=16.86;ReadPosRankSum=-0.72;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,49 1/1:0,4:4:12:99,12,0 chr1 1530253 . C T 94.02 PASS AC=4;AF=1;AN=4;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=31.34;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:2:4,2,0 1/1:0,2:2:9:115,9,0 -chr1 1530270 rs34595829 G GAC 84.98 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=14.16;normal_af=1;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:2:4,2,0 1/1:0,2:2:9:115,9,0 -chr1 1530686 rs150408813 CAG C 45.13 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=11.28;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:80,6,0 +chr1 1530270 rs34595829 G GAC 84.98 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=14.16;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:2:4,2,0 1/1:0,2:2:9:115,9,0 +chr1 1530686 rs150408813 CAG C 45.13 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=11.28;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:80,6,0 chr1 1543010 rs9442420 T C 64.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=21.61;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,1:1:3:41,3,0 chr1 1551927 rs7418389 T C 5843.2 PASS AC=4;AF=1;AN=4;BaseQRankSum=2.062;ClippingRankSum=-0.224;DB;DP=203;FS=0;MLEAC=4;MLEAF=1;MQ=55.43;MQ0=0;MQRankSum=0.647;QD=28.78;ReadPosRankSum=0.079;normal_af=1.0;normal_ac=21;normal_dp=21 GT:AD:DP:GQ:PL 1/1:2,86:88:99:2542,215,0 1/1:0,115:115:99:3328,345,0 chr1 1557675 rs28710339 G C 108.99 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=6;FS=0;MLEAC=3;MLEAF=0.75;MQ=60;MQ0=0;MQRankSum=0.736;QD=18.16;ReadPosRankSum=-0.736;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:1,1:2:4:37,0,4 1/1:0,4:4:12:99,12,0 @@ -275,7 +275,7 @@ chr1 1566068 rs28730454 A G 51.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF chr1 1571640 . G T 138.02 PASS AC=4;AF=1;AN=4;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=29.34;MQ0=0;QD=27.6;normal_af=0.4444444444444444;normal_ac=4;normal_dp=9 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 1/1:0,3:3:9:96,9,0 chr1 1574019 rs9442412 A G 3621.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.03;ClippingRankSum=0.005;DB;DP=486;FS=1.16;MLEAC=2;MLEAF=0.5;MQ=34;MQ0=0;MQRankSum=-2.721;QD=7.45;ReadPosRankSum=0.661;normal_af=0.3488372093023256;normal_ac=30;normal_dp=86 GT:AD:DP:GQ:PL 0/1:144,86:230:99:1621,0,3294 0/1:154,102:256:99:2029,0,3541 chr1 1574076 rs9442413 G A 1312.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.691;ClippingRankSum=-0.683;DB;DP=142;FS=8.193;MLEAC=2;MLEAF=0.5;MQ=43.11;MQ0=0;MQRankSum=-1.791;QD=9.24;ReadPosRankSum=-1.637;normal_af=0.4166666666666667;normal_ac=10;normal_dp=24 GT:AD:DP:GQ:PL 0/1:40,28:68:99:633,0,1110 0/1:44,30:74:99:708,0,1144 -chr1 1574775 . CT C 46.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=23.07;normal_af=1;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 ./.:.:.:.:. +chr1 1574775 . CT C 46.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=23.07;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 ./.:.:.:.:. chr1 1575616 rs80012316 T C 985.17 PASS AC=4;AF=1;AN=4;BaseQRankSum=-0.983;ClippingRankSum=-0.796;DB;DP=37;FS=0;MLEAC=4;MLEAF=1;MQ=30.49;MQ0=0;MQRankSum=-1.733;QD=26.63;ReadPosRankSum=0.328;normal_af=0.9230769230769231;normal_ac=12;normal_dp=13 GT:AD:DP:GQ:PL 1/1:1,13:14:3:331,3,0 1/1:0,23:23:69:680,69,0 chr1 1575836 rs72468213 C G 1909.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=8.472;ClippingRankSum=-0.88;DB;DP=313;FS=2.554;MLEAC=2;MLEAF=0.5;MQ=26.01;MQ0=0;MQRankSum=-2.398;QD=6.1;ReadPosRankSum=2.646;normal_af=0.35365853658536583;normal_ac=29;normal_dp=82 GT:AD:DP:GQ:PL 0/1:115,56:171:99:1023,0,2719 0/1:94,48:142:99:915,0,2296 chr1 1576636 rs3765908 G A 4779.2 PASS AC=4;AF=1;AN=4;DB;DP=138;FS=0;MLEAC=4;MLEAF=1;MQ=52.95;MQ0=0;QD=34.63;normal_af=1.0;normal_ac=30;normal_dp=30 GT:AD:DP:GQ:PL 1/1:0,67:67:99:2325,202,0 1/1:0,71:71:99:2481,214,0 @@ -288,7 +288,7 @@ chr1 1590526 rs9329573 G C 689.23 PASS AC=4;AF=1;AN=4;DB;DP=20;FS=0;MLEAC=4;MLEA chr1 1590575 rs9661285 G A 182.26 PASS AC=4;AF=1;AN=4;DB;DP=6;FS=0;MLEAC=4;MLEAF=1;MQ=56.82;MQ0=0;QD=30.38;normal_af=1.0;normal_ac=4;normal_dp=4 GT:AD:DP:GQ:PL 1/1:0,5:5:15:172,15,0 1/1:0,1:1:3:36,3,0 chr1 1592881 rs4648774 A C 382.33 PASS AC=4;AF=1;AN=4;DB;DP=14;FS=0;MLEAC=4;MLEAF=1;MQ=25.48;MQ0=0;QD=27.31;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:122,12,0 1/1:0,10:10:30:287,30,0 chr1 1593023 rs114362359 G C 42.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=29;MQ0=0;QD=21.09;normal_af=1.0;normal_ac=3;normal_dp=3 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:68,6,0 -chr1 1594199 . C CT 1829.16 PASS AC=4;AF=1;AN=4;DP=50;FS=0;MLEAC=4;MLEAF=1;MQ=51.31;MQ0=0;QD=35.48;normal_af=0.818182;normal_ac=9;normal_dp=11 GT:AD:DP:GQ:PL 1/1:0,24:24:72:895,72,0 1/1:0,26:26:78:970,78,0 +chr1 1594199 . C CT 1829.16 PASS AC=4;AF=1;AN=4;DP=50;FS=0;MLEAC=4;MLEAF=1;MQ=51.31;MQ0=0;QD=35.48;normal_af=0.8181818181818182;normal_ac=9;normal_dp=11 GT:AD:DP:GQ:PL 1/1:0,24:24:72:895,72,0 1/1:0,26:26:78:970,78,0 chr1 1594315 rs1061892 C T 4292.2 PASS AC=4;AF=1;AN=4;DB;DP=119;FS=0;MLEAC=4;MLEAF=1;MQ=54.85;MQ0=0;QD=28.39;normal_af=1.0;normal_ac=21;normal_dp=21 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1621,132,0 1/1:0,75:75:99:2698,225,0 chr1 1594393 rs141732428 T A 1969.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.342;ClippingRankSum=-0.536;DB;DP=150;FS=0;MLEAC=2;MLEAF=0.5;MQ=52.93;MQ0=0;MQRankSum=-1.631;QD=13.13;ReadPosRankSum=0.623;normal_af=0.45161290322580644;normal_ac=14;normal_dp=31 GT:AD:DP:GQ:PL 0/1:34,34:68:99:882,0,861 0/1:38,44:82:99:1116,0,1035 chr1 1594498 rs7416520 C T 2457.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=4.931;ClippingRankSum=2.713;DB;DP=232;FS=7.975;MLEAC=2;MLEAF=0.5;MQ=52.42;MQ0=0;MQRankSum=-7.338;QD=10.59;ReadPosRankSum=2.332;normal_af=0.36538461538461536;normal_ac=19;normal_dp=52 GT:AD:DP:GQ:PL 0/1:63,46:109:99:1224,0,1740 0/1:75,48:123:99:1262,0,2024 @@ -309,16 +309,16 @@ chr1 1602787 rs4639697 G T 263.75 PASS AC=4;AF=1;AN=4;DB;DP=8;FS=0;MLEAC=4;MLEAF chr1 1608229 rs143080014 C T 1183.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.884;ClippingRankSum=-0.641;DB;DP=96;FS=3.851;MLEAC=2;MLEAF=0.5;MQ=29.28;MQ0=0;MQRankSum=-0.39;QD=12.33;ReadPosRankSum=2.041;normal_af=0.3783783783783784;normal_ac=14;normal_dp=37 GT:AD:DP:GQ:PL 0/1:19,29:48:99:682,0,365 0/1:24,24:48:99:530,0,558 chr1 1608394 rs146877222 C T 642.2 PASS AC=4;AF=1;AN=4;DB;DP=25;FS=0;MLEAC=4;MLEAF=1;MQ=22;MQ0=0;QD=25.69;normal_af=0.8666666666666667;normal_ac=13;normal_dp=15 GT:AD:DP:GQ:PL 1/1:0,12:12:36:321,36,0 1/1:0,13:13:39:348,39,0 chr1 1623725 rs151167524 C A 190.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-3.224;ClippingRankSum=-0.144;DB;DP=17;FS=0;MLEAC=2;MLEAF=0.5;MQ=25.35;MQ0=0;MQRankSum=1.299;QD=11.2;ReadPosRankSum=0.818;normal_af=0.375;normal_ac=3;normal_dp=8 GT:AD:DP:GQ:PL 0/1:4,5:9:80:120,0,80 0/1:4,4:8:90:99,0,90 -chr1 1633003 . C CCG 84.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.817;ClippingRankSum=-0.938;DP=26;FS=4.224;MLEAC=2;MLEAF=0.5;MQ=37.72;MQ0=0;MQRankSum=0.757;QD=1.62;ReadPosRankSum=-0.333;normal_af=0.142857;normal_ac=1;normal_dp=7 GT:AD:DP:GQ:PL 0/1:9,3:12:50:50,0,380 0/1:10,4:14:72:72,0,421 +chr1 1633003 . C CCG 84.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.817;ClippingRankSum=-0.938;DP=26;FS=4.224;MLEAC=2;MLEAF=0.5;MQ=37.72;MQ0=0;MQRankSum=0.757;QD=1.62;ReadPosRankSum=-0.333;normal_af=0.0;normal_ac=0;normal_dp=7 GT:AD:DP:GQ:PL 0/1:9,3:12:50:50,0,380 0/1:10,4:14:72:72,0,421 chr1 1635004 rs874516 T C 1800.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=6.283;ClippingRankSum=-1.859;DB;DP=129;FS=5.555;MLEAC=2;MLEAF=0.5;MQ=52;MQ0=0;MQRankSum=-0.624;QD=13.96;ReadPosRankSum=1.623;normal_af=0.4782608695652174;normal_ac=11;normal_dp=23 GT:AD:DP:GQ:PL 0/1:37,30:67:99:862,0,863 0/1:29,33:62:99:967,0,723 chr1 1635619 rs2076329 T C 3344.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-5.674;ClippingRankSum=-0.211;DB;DP=258;FS=5.107;MLEAC=2;MLEAF=0.5;MQ=56.13;MQ0=0;MQRankSum=-1.599;QD=12.96;ReadPosRankSum=-1.199;normal_af=0.5;normal_ac=23;normal_dp=46 GT:AD:DP:GQ:PL 0/1:54,66:120:99:1741,0,1555 0/1:74,64:138:99:1632,0,2093 chr1 1635749 rs55880629 C A 2846.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.243;ClippingRankSum=3.254;DB;DP=377;FS=11.771;MLEAC=2;MLEAF=0.5;MQ=47.83;MQ0=0;MQRankSum=-7.663;QD=7.55;ReadPosRankSum=1.795;normal_af=0.2641509433962264;normal_ac=14;normal_dp=53 GT:AD:DP:GQ:PL 0/1:107,51:158:99:1078,0,2776 0/1:136,83:219:99:1797,0,3434 chr1 1636044 rs1059822 G A 727.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.545;ClippingRankSum=2.729;DB;DP=192;FS=2.191;MLEAC=2;MLEAF=0.5;MQ=48.48;MQ0=0;MQRankSum=-4.526;QD=3.79;ReadPosRankSum=-0.187;normal_af=0.41379310344827586;normal_ac=12;normal_dp=29 GT:AD:DP:GQ:PL 0/1:67,20:87:99:345,0,1611 0/1:82,23:105:99:411,0,2102 chr1 1636274 rs2179381 C T 199.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.468;ClippingRankSum=0.825;DB;DP=12;FS=3.09;MLEAC=2;MLEAF=0.5;MQ=47.22;MQ0=0;MQRankSum=0.289;QD=16.62;ReadPosRankSum=-1.134;normal_af=1.0;normal_ac=4;normal_dp=4 GT:AD:DP:GQ:PL 0/1:2,6:8:47:174,0,47 0/1:2,2:4:54:54,0,60 chr1 1636330 rs192815888 G A 825.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-5.219;ClippingRankSum=1.343;DB;DP=57;FS=9.099;MLEAC=2;MLEAF=0.5;MQ=49.33;MQ0=0;MQRankSum=0.137;QD=14.48;ReadPosRankSum=-1.311;normal_af=0.6666666666666666;normal_ac=8;normal_dp=12 GT:AD:DP:GQ:PL 0/1:9,23:32:99:635,0,254 0/1:16,9:25:99:219,0,504 -chr1 1637506 rs70937176 ACT A 94.91 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0;MLEAC=2;MLEAF=0.5;MQ=42.61;MQ0=0;MQRankSum=-1.231;QD=15.82;ReadPosRankSum=0.358;normal_af=1;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 0/0:2,0:2:6:0,6,91 +chr1 1637506 rs70937176 ACT A 94.91 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0;MLEAC=2;MLEAF=0.5;MQ=42.61;MQ0=0;MQRankSum=-1.231;QD=15.82;ReadPosRankSum=0.358;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 0/0:2,0:2:6:0,6,91 chr1 1639801 rs74378830 T C 1719.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.457;ClippingRankSum=-0.34;DB;DP=381;FS=2.002;MLEAC=2;MLEAF=0.5;MQ=48.03;MQ0=0;MQRankSum=-11.624;QD=4.51;ReadPosRankSum=5.991;normal_af=0.4507042253521127;normal_ac=32;normal_dp=71 GT:AD:DP:GQ:PL 0/1:134,59:193:99:1021,0,3414 0/1:140,48:188:99:727,0,3683 -chr1 1647649 rs70937179 C CT 46.13 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=23.07;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:81,6,0 +chr1 1647649 rs70937179 C CT 46.13 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=23.07;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:81,6,0 chr1 1648493 rs72634831 T C 63.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=45.96;MQ0=0;QD=21.24;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:90,9,0 chr1 1649619 rs140903459 A G 170.33 PASS AC=2;AF=1;AN=2;DB;DP=5;FS=0;MLEAC=2;MLEAF=1;MQ=56.16;MQ0=0;QD=34.07;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,5:5:15:197,15,0 ./.:.:.:.:. chr1 1649632 rs76854454 C T 170.33 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=32.12;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,3:3:15:197,15,0 ./.:.:.:.:. @@ -330,34 +330,34 @@ chr1 1650807 rs1137005 T C 800.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.222;Clipp chr1 1650832 rs72909030 A G 1047.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.196;ClippingRankSum=0.196;DB;DP=78;FS=0.864;MLEAC=2;MLEAF=0.5;MQ=55.27;MQ0=0;MQRankSum=-1.658;QD=13.43;ReadPosRankSum=-0.65;normal_af=0.6153846153846154;normal_ac=8;normal_dp=13 GT:AD:DP:GQ:PL 0/1:9,28:37:99:656,0,171 0/1:25,16:41:99:420,0,566 chr1 1650845 rs1059831 G A 750.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-1.852;ClippingRankSum=-0.136;DB;DP=80;FS=0.84;MLEAC=2;MLEAF=0.5;MQ=55.08;MQ0=0;MQRankSum=3.084;QD=9.38;ReadPosRankSum=0.834;normal_af=0.38461538461538464;normal_ac=5;normal_dp=13 GT:AD:DP:GQ:PL 0/1:27,10:37:99:185,0,674 0/1:18,25:43:99:594,0,447 chr1 1650920 rs36191908 G A 518.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.8;ClippingRankSum=-0.014;DB;DP=40;FS=3.01;MLEAC=2;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.204;QD=12.96;ReadPosRankSum=0.419;normal_af=0.4444444444444444;normal_ac=4;normal_dp=9 GT:AD:DP:GQ:PL 0/1:9,9:18:99:244,0,286 0/1:11,11:22:99:303,0,331 -chr1 1650938 . CGG C 274.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.308;ClippingRankSum=-1.838;DP=16;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-3.413;QD=8.58;ReadPosRankSum=-1.733;normal_af=0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 0/1:5,1:6:27:27,0,448 0/1:3,7:10:99:285,0,247 -chr1 1650942 . A AAG 274.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.308;ClippingRankSum=-1.628;DP=16;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-3.413;QD=8.58;ReadPosRankSum=-2.048;normal_af=0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 0/1:5,1:6:27:27,0,448 0/1:3,7:10:99:285,0,247 +chr1 1650938 . CGG C 274.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.308;ClippingRankSum=-1.838;DP=16;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-3.413;QD=8.58;ReadPosRankSum=-1.733;normal_af=0.0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 0/1:5,1:6:27:27,0,448 0/1:3,7:10:99:285,0,247 +chr1 1650942 . A AAG 274.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=3.308;ClippingRankSum=-1.628;DP=16;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-3.413;QD=8.58;ReadPosRankSum=-2.048;normal_af=0.0;normal_ac=0;normal_dp=3 GT:AD:DP:GQ:PL 0/1:5,1:6:27:27,0,448 0/1:3,7:10:99:285,0,247 chr1 1650960 rs72634834 G A 81.37 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-2.637;ClippingRankSum=-1.835;DB;DP=12;FS=0;MLEAC=1;MLEAF=0.25;MQ=51.77;MQ0=0;MQRankSum=-2.637;QD=11.62;ReadPosRankSum=-1.599;normal_af=0.0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,191 0/1:3,4:7:99:111,0,99 chr1 1650996 rs74223875 T C 68.41 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=6.021;MLEAC=1;MLEAF=0.25;MQ=53.95;MQ0=0;MQRankSum=-0.727;QD=22.8;ReadPosRankSum=0.727;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 0/1:2,1:3:92:96,0,92 0/0:1,0:1:3:0,3,74 chr1 1651003 rs76941027 G A 68.41 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-1.231;ClippingRankSum=0.358;DB;DP=5;FS=0;MLEAC=1;MLEAF=0.25;MQ=44.1;MQ0=0;MQRankSum=-1.231;QD=17.1;ReadPosRankSum=-1.231;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 0/1:1,3:4:92:96,0,92 0/0:1,0:1:3:0,3,74 chr1 1651047 rs72909034 C T 115.25 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=28.81;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:10:104,10,0 1/1:0,1:1:4:37,4,0 -chr1 1651062 . T TC 99.05 PASS AC=4;AF=1;AN=4;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=24.76;normal_af=0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:6:91,6,0 1/1:0,1:1:2:42,2,0 -chr1 1651065 . T TTTTTC 99.05 PASS AC=4;AF=1;AN=4;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=4.95;normal_af=0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:6:91,6,0 1/1:0,1:1:2:42,2,0 -chr1 1651077 . CGG C 102.59 PASS AC=4;AF=1;AN=4;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=17.1;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:91,6,0 1/1:0,1:1:4:46,4,0 +chr1 1651062 . T TC 99.05 PASS AC=4;AF=1;AN=4;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=24.76;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:6:91,6,0 1/1:0,1:1:2:42,2,0 +chr1 1651065 . T TTTTTC 99.05 PASS AC=4;AF=1;AN=4;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=4.95;normal_af=0.0;normal_ac=0;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:6:91,6,0 1/1:0,1:1:2:42,2,0 +chr1 1651077 . CGG C 102.59 PASS AC=4;AF=1;AN=4;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=17.1;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:6:91,6,0 1/1:0,1:1:4:46,4,0 chr1 1651093 . C T 70.97 PASS AC=4;AF=1;AN=4;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=23.66;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:4:48,4,0 1/1:0,1:1:4:48,4,0 chr1 1651094 . A G 70.97 PASS AC=4;AF=1;AN=4;DP=2;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=24.92;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:4:48,4,0 1/1:0,1:1:4:48,4,0 chr1 1651098 . A G 70.97 PASS AC=4;AF=1;AN=4;DP=1;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=29.27;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:.:.:4:48,4,0 1/1:0,1:1:4:48,4,0 chr1 1651103 rs36153776 G A 70.97 PASS AC=4;AF=1;AN=4;DB;DP=1;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=29.86;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:.:.:4:48,4,0 1/1:0,1:1:4:48,4,0 chr1 1651104 . G T 70.97 PASS AC=4;AF=1;AN=4;DP=1;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=30.29;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:.:.:4:48,4,0 1/1:0,1:1:4:48,4,0 -chr1 1651108 . GTA G 61.93 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 -chr1 1651111 . GA G 61.93 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 -chr1 1651114 . ACG A 61.93 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 +chr1 1651108 . GTA G 61.93 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0.0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 +chr1 1651111 . GA G 61.93 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0.0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 +chr1 1651114 . ACG A 61.93 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0.0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 chr1 1651126 . A C 70.97 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0.0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 chr1 1651136 . C T 70.97 PASS AC=4;AF=1;AN=4;DP=0;FS=0;MLEAC=4;MLEAF=1;MQ=0;MQ0=0;normal_af=0.0;normal_ac=0;normal_dp=0 GT:GQ:PL 1/1:4:48,4,0 1/1:4:48,4,0 chr1 1653799 rs2223485 C T 691.2 PASS AC=4;AF=1;AN=4;DB;DP=22;FS=0;MLEAC=4;MLEAF=1;MQ=39.5;MQ0=0;QD=31.42;normal_af=1.0;normal_ac=5;normal_dp=5 GT:AD:DP:GQ:PL 1/1:0,13:13:39:438,39,0 1/1:0,9:9:27:280,27,0 chr1 1653885 rs61777493 C A 3006.2 PASS AC=4;AF=1;AN=4;DB;DP=91;FS=0;MLEAC=4;MLEAF=1;MQ=45.6;MQ0=0;QD=33.04;normal_af=1.0;normal_ac=17;normal_dp=17 GT:AD:DP:GQ:PL 1/1:0,40:40:99:1406,120,0 1/1:0,51:51:99:1627,153,0 -chr1 1654004 . A ATTTGAATATTTTTGTTAATTT 206.06 PASS AC=2;AF=0.5;AN=4;DP=8;FS=0;MLEAC=2;MLEAF=0.5;MQ=30.9;MQ0=0;QD=1.23;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:0,2:2:10:96,0,10 0/1:0,4:4:10:147,0,10 +chr1 1654004 . A ATTTGAATATTTTTGTTAATTT 206.06 PASS AC=2;AF=0.5;AN=4;DP=8;FS=0;MLEAC=2;MLEAF=0.5;MQ=30.9;MQ0=0;QD=1.23;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:0,2:2:10:96,0,10 0/1:0,4:4:10:147,0,10 chr1 1654013 rs74045997 C G 215.1 PASS AC=2;AF=0.5;AN=4;DB;DP=7;FS=0;MLEAC=2;MLEAF=0.5;MQ=29;MQ0=0;QD=30.73;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:0,3:3:10:96,0,10 0/1:0,4:4:10:147,0,10 chr1 1654038 rs61777494 G A 345.3 PASS AC=4;AF=1;AN=4;DB;DP=11;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=31.39;normal_af=0.5;normal_ac=1;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,5:5:15:169,15,0 1/1:0,6:6:18:203,18,0 chr1 1654058 rs61777495 C T 1413.2 PASS AC=4;AF=1;AN=4;DB;DP=13;FS=0;MLEAC=4;MLEAF=1;MQ=32.45;MQ0=0;QD=31.18;normal_af=0.6666666666666666;normal_ac=2;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,6:6:42:590,42,0 1/1:0,7:7:60:850,60,0 chr1 1654064 rs200615789 A T 1413.2 PASS AC=4;AF=1;AN=4;DB;DP=32;FS=0;MLEAC=4;MLEAF=1;MQ=42.7;MQ0=0;QD=25.84;normal_af=0.5;normal_ac=1;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,13:13:42:590,42,0 1/1:0,19:19:60:850,60,0 chr1 1654065 rs35174499 AGCG A 1404.16 PASS AC=4;AF=1;AN=4;DB;DP=32;FS=0;MLEAC=4;MLEAF=1;MQ=42.7;MQ0=0;QD=14.63;normal_af=0.5;normal_ac=1;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,13:13:42:590,42,0 1/1:0,19:19:60:850,60,0 -chr1 1654379 rs200326357 TAAG T 192.08 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=33.38;MQ0=0;QD=12.81;normal_af=0.666667;normal_ac=2;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,4:4:13:181,13,0 1/1:0,1:1:4:46,4,0 +chr1 1654379 rs200326357 TAAG T 192.08 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=33.38;MQ0=0;QD=12.81;normal_af=0.6666666666666666;normal_ac=2;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,4:4:13:181,13,0 1/1:0,1:1:4:46,4,0 chr1 1655474 rs142552274 G A 98.33 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0;MLEAC=1;MLEAF=0.5;MQ=32.72;MQ0=0;MQRankSum=0.731;QD=19.67;ReadPosRankSum=-0.731;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 0/1:1,4:5:15:125,0,15 ./.:.:.:.:. chr1 1655928 rs28649027 G C 142.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.53;ClippingRankSum=2.652;DB;DP=15;FS=3.979;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.059;QD=9.5;ReadPosRankSum=-1.827;normal_af=0.25;normal_ac=1;normal_dp=4 GT:AD:DP:GQ:PL 0/1:6,3:9:99:99,0,213 0/1:3,3:6:72:72,0,99 chr1 1658945 rs144604384 T C 3143.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.348;ClippingRankSum=1.22;DB;DP=268;FS=22.488;MLEAC=2;MLEAF=0.5;MQ=30.62;MQ0=0;MQRankSum=3.636;QD=11.73;ReadPosRankSum=-1.461;normal_af=0.4142857142857143;normal_ac=29;normal_dp=70 GT:AD:DP:GQ:PL 0/1:64,54:118:99:1278,0,1388 0/1:69,81:150:99:1894,0,1412 @@ -371,7 +371,7 @@ chr1 1661844 rs61777505 G C 9853.2 PASS AC=4;AF=1;AN=4;BaseQRankSum=-0.351;Clipp chr1 1662315 rs144341301 C G 2471.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.44;ClippingRankSum=0.174;DB;DP=237;FS=5.439;MLEAC=2;MLEAF=0.5;MQ=36.57;MQ0=0;MQRankSum=-0.381;QD=10.43;ReadPosRankSum=2.845;normal_af=0.42028985507246375;normal_ac=29;normal_dp=69 GT:AD:DP:GQ:PL 0/1:67,58:125:99:1327,0,1546 0/1:61,51:112:99:1173,0,1489 chr1 1662428 rs2281171 A G 1170.2 PASS AC=4;AF=1;AN=4;DB;DP=32;FS=0;MLEAC=4;MLEAF=1;MQ=43.09;MQ0=0;QD=30.65;normal_af=1.0;normal_ac=9;normal_dp=9 GT:AD:DP:GQ:PL 1/1:0,17:17:51:642,51,0 1/1:0,15:15:45:555,45,0 chr1 1663605 rs66653340 A G 397.34 PASS AC=4;AF=1;AN=4;DB;DP=12;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=33.11;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:138,12,0 1/1:0,8:8:24:286,24,0 -chr1 1663696 . G GT 36.19 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-1.444;ClippingRankSum=-1.217;DP=97;FS=0;MLEAC=1;MLEAF=0.25;MQ=57.73;MQ0=0;MQRankSum=-0.33;QD=0.71;ReadPosRankSum=0.268;normal_af=0;normal_ac=0;normal_dp=14 GT:AD:DP:GQ:PL 0/0:30,3:33:21:0,21,724 0/1:27,9:36:75:75,0,622 +chr1 1663696 . G GT 36.19 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-1.444;ClippingRankSum=-1.217;DP=97;FS=0;MLEAC=1;MLEAF=0.25;MQ=57.73;MQ0=0;MQRankSum=-0.33;QD=0.71;ReadPosRankSum=0.268;normal_af=0.0;normal_ac=0;normal_dp=14 GT:AD:DP:GQ:PL 0/0:30,3:33:21:0,21,724 0/1:27,9:36:75:75,0,622 chr1 1663831 rs3817856 C T 7270.2 PASS AC=4;AF=1;AN=4;DB;DP=238;FS=0;MLEAC=4;MLEAF=1;MQ=58.3;MQ0=0;QD=30.55;normal_af=1.0;normal_ac=39;normal_dp=39 GT:AD:DP:GQ:PL 1/1:0,129:129:99:3935,387,0 1/1:0,109:109:99:3362,327,0 chr1 1664019 rs2294488 T C 124.52 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=31.13;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,1:1:3:35,3,0 1/1:0,3:3:9:115,9,0 chr1 1666175 rs61777509 C T 1577.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-3.125;ClippingRankSum=0.654;DB;DP=188;FS=4.215;MLEAC=2;MLEAF=0.5;MQ=30.82;MQ0=0;MQRankSum=3.177;QD=8.39;ReadPosRankSum=-1.476;normal_af=0.3088235294117647;normal_ac=21;normal_dp=68 GT:AD:DP:GQ:PL 0/1:49,50:99:99:1031,0,1051 0/1:58,30:88:99:575,0,1284 @@ -383,7 +383,7 @@ chr1 1667371 rs1474649 A G 1199.2 PASS AC=4;AF=1;AN=4;DB;DP=32;FS=0;MLEAC=4;MLEA chr1 1667419 rs2377208 A C 316.17 PASS AC=4;AF=1;AN=4;DB;DP=10;FS=0;MLEAC=4;MLEAF=1;MQ=54.64;MQ0=0;QD=31.62;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:36,3,0 1/1:0,9:9:27:306,27,0 chr1 1668943 rs28537345 A C 72.31 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=46;MQ0=0;QD=18.08;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,2:2:6:49,6,0 chr1 1669734 rs80140081 G T 1963.2 PASS AC=4;AF=1;AN=4;DB;DP=62;FS=0;MLEAC=4;MLEAF=1;MQ=36.52;MQ0=0;QD=31.66;normal_af=0.8181818181818182;normal_ac=9;normal_dp=11 GT:AD:DP:GQ:PL 1/1:0,19:19:57:608,57,0 1/1:0,43:43:99:1382,129,0 -chr1 1669844 . CCA C 814.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.158;ClippingRankSum=1.664;DP=46;FS=0;MLEAC=2;MLEAF=0.5;MQ=34.11;MQ0=0;MQRankSum=1.178;QD=8.85;ReadPosRankSum=0.62;normal_af=0.197917;normal_ac=19;normal_dp=96 GT:AD:DP:GQ:PL 0/1:10,5:15:99:169,0,410 0/1:11,17:28:99:683,0,415 +chr1 1669844 . CCA C 814.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.158;ClippingRankSum=1.664;DP=46;FS=0;MLEAC=2;MLEAF=0.5;MQ=34.11;MQ0=0;MQRankSum=1.178;QD=8.85;ReadPosRankSum=0.62;normal_af=0.19791666666666666;normal_ac=19;normal_dp=96 GT:AD:DP:GQ:PL 0/1:10,5:15:99:169,0,410 0/1:11,17:28:99:683,0,415 chr1 1670036 . C A 374.21 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=-1.739;ClippingRankSum=1.107;DP=11;FS=10.414;MLEAC=3;MLEAF=0.75;MQ=31.86;MQ0=0;MQRankSum=1.423;QD=34.02;ReadPosRankSum=-1.739;normal_af=0.7;normal_ac=14;normal_dp=20 GT:AD:DP:GQ:PL 0/1:1,2:3:44:81,0,44 1/1:0,8:8:24:323,24,0 chr1 1670045 rs200217868 C T 374.21 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=-0.747;ClippingRankSum=0.747;DB;DP=8;FS=9.031;MLEAC=3;MLEAF=0.75;MQ=30.17;MQ0=0;MQRankSum=0.747;QD=28.93;ReadPosRankSum=0.747;normal_af=0.6190476190476191;normal_ac=13;normal_dp=21 GT:AD:DP:GQ:PL 0/1:1,2:3:44:81,0,44 1/1:0,5:5:24:323,24,0 chr1 1670958 rs146637450 C G 160.79 PASS AC=4;AF=1;AN=4;DB;DP=7;FS=0;MLEAC=4;MLEAF=1;MQ=22;MQ0=0;QD=22.97;normal_af=0.5119047619047619;normal_ac=43;normal_dp=84 GT:AD:DP:GQ:PL 1/1:0,5:5:15:134,15,0 1/1:0,2:2:6:53,6,0 @@ -401,7 +401,7 @@ chr1 1688469 rs4648623 C G 7040.2 PASS AC=4;AF=1;AN=4;BaseQRankSum=1.703;Clippin chr1 1688513 rs4648624 G T 11709.2 PASS AC=4;AF=1;AN=4;DB;DP=433;FS=0;MLEAC=4;MLEAF=1;MQ=55.48;MQ0=0;QD=27.04;normal_af=1.0;normal_ac=44;normal_dp=44 GT:AD:DP:GQ:PL 1/1:0,196:196:99:5314,588,0 1/1:0,236:236:99:6422,707,0 chr1 1691764 rs72634842 G A 93.52 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=23.38;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:35,3,0 1/1:0,3:3:9:84,9,0 chr1 1694103 rs2011384 A G 72.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=18.12;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,4:4:12:99,12,0 -chr1 1694198 rs145189624 AAATG A 100.8 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=8.4;normal_af=1;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,2:2:6:90,6,0 +chr1 1694198 rs145189624 AAATG A 100.8 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=8.4;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 1/1:0,2:2:6:90,6,0 chr1 1696659 rs75906779 A G 623.21 PASS AC=4;AF=1;AN=4;DB;DP=18;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=34.62;normal_af=1.0;normal_ac=3;normal_dp=3 GT:AD:DP:GQ:PL 1/1:0,8:8:24:290,24,0 1/1:0,10:10:30:360,30,0 chr1 1722828 rs3737627 G A 61.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=45.96;MQ0=0;QD=20.57;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:88,9,0 chr1 1725261 rs7545812 A G 148.75 PASS AC=4;AF=1;AN=4;DB;DP=6;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=24.79;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 1/1:0,3:3:9:88,9,0 @@ -422,23 +422,23 @@ chr1 1851936 rs2474458 C A 61.84 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF= chr1 1859558 rs28670388 T C 61.93 PASS AC=4;AF=1;AN=4;DB;DP=3;FS=0;MLEAC=4;MLEAF=1;MQ=45.96;MQ0=0;QD=20.64;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 1/1:0,1:1:3:10,3,0 chr1 1863405 rs60147457 T C 96.52 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=49.84;MQ0=0;QD=24.13;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:84,9,0 1/1:0,1:1:3:38,3,0 chr1 1870210 rs2803323 G A 110.02 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=52.03;MQ0=0;QD=22;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 1/1:0,2:2:6:49,6,0 -chr1 1870653 . A ATG 36.79 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0;ClippingRankSum=0;DP=6;FS=0;MLEAC=2;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=1.026;QD=4.6;ReadPosRankSum=-1.026;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,77 1/1:0,2:2:6:76,6,0 +chr1 1870653 . A ATG 36.79 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0;ClippingRankSum=0;DP=6;FS=0;MLEAC=2;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=1.026;QD=4.6;ReadPosRankSum=-1.026;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,77 1/1:0,2:2:6:76,6,0 chr1 1873625 rs12758705 G A 59.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=19.9;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:86,9,0 chr1 1874837 rs2803330 A G 63.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=21.24;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 ./.:.:.:.:. -chr1 1880491 rs202218537 TTTCC T 134.42 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=56.88;MQ0=0;QD=8.4;normal_af=1;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:170,12,0 ./.:.:.:.:. +chr1 1880491 rs202218537 TTTCC T 134.42 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=56.88;MQ0=0;QD=8.4;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:170,12,0 ./.:.:.:.:. chr1 1882287 rs2490540 A G 114.35 PASS AC=4;AF=1;AN=4;DB;DP=5;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=22.87;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 1/1:0,1:1:3:41,3,0 -chr1 1886204 rs112927199 A AGAGT 502.3 PASS AC=4;AF=1;AN=4;DB;DP=11;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=11.42;normal_af=1;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:179,12,0 1/1:0,7:7:23:359,23,0 +chr1 1886204 rs112927199 A AGAGT 502.3 PASS AC=4;AF=1;AN=4;DB;DP=11;FS=0;MLEAC=4;MLEAF=1;MQ=29;MQ0=0;QD=11.42;normal_af=0.0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:179,12,0 1/1:0,7:7:23:359,23,0 chr1 1886220 rs4648738 C T 513.34 PASS AC=4;AF=1;AN=4;DB;DP=12;FS=0;MLEAC=4;MLEAF=1;MQ=29.55;MQ0=0;QD=27.7;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 1/1:0,8:8:24:360,24,0 chr1 1886222 rs2803287 T G 513.34 PASS AC=4;AF=1;AN=4;DB;DP=12;FS=0;MLEAC=4;MLEAF=1;MQ=29.55;MQ0=0;QD=34.12;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 1/1:0,8:8:24:360,24,0 -chr1 1886345 rs200873200 C CA 4845.16 PASS AC=4;AF=1;AN=4;BaseQRankSum=0.693;ClippingRankSum=-0.976;DB;DP=110;FS=0;MLEAC=4;MLEAF=1;MQ=51.07;MQ0=0;MQRankSum=-1.039;QD=28.51;ReadPosRankSum=-0.189;normal_af=0;normal_ac=0;normal_dp=17 GT:AD:DP:GQ:PL 1/1:1,40:41:33:1704,33,0 1/1:0,69:69:99:3177,211,0 -chr1 1886346 rs76908344 G GCC 4845.16 PASS AC=4;AF=1;AN=4;BaseQRankSum=0.835;ClippingRankSum=-0.495;DB;DP=112;FS=0;MLEAC=4;MLEAF=1;MQ=51.24;MQ0=0;MQRankSum=-0.959;QD=21.63;ReadPosRankSum=-0.124;normal_af=0;normal_ac=0;normal_dp=17 GT:AD:DP:GQ:PL 1/1:1,40:41:33:1704,33,0 1/1:0,71:71:99:3177,211,0 +chr1 1886345 rs200873200 C CA 4845.16 PASS AC=4;AF=1;AN=4;BaseQRankSum=0.693;ClippingRankSum=-0.976;DB;DP=110;FS=0;MLEAC=4;MLEAF=1;MQ=51.07;MQ0=0;MQRankSum=-1.039;QD=28.51;ReadPosRankSum=-0.189;normal_af=0.0;normal_ac=0;normal_dp=17 GT:AD:DP:GQ:PL 1/1:1,40:41:33:1704,33,0 1/1:0,69:69:99:3177,211,0 +chr1 1886346 rs76908344 G GCC 4845.16 PASS AC=4;AF=1;AN=4;BaseQRankSum=0.835;ClippingRankSum=-0.495;DB;DP=112;FS=0;MLEAC=4;MLEAF=1;MQ=51.24;MQ0=0;MQRankSum=-0.959;QD=21.63;ReadPosRankSum=-0.124;normal_af=0.0;normal_ac=0;normal_dp=17 GT:AD:DP:GQ:PL 1/1:1,40:41:33:1704,33,0 1/1:0,71:71:99:3177,211,0 chr1 1886385 rs2803286 T C 8992.2 PASS AC=4;AF=1;AN=4;BaseQRankSum=0.931;ClippingRankSum=-0.06;DB;DP=328;FS=1.529;MLEAC=4;MLEAF=1;MQ=49.21;MQ0=0;MQRankSum=0.6;QD=27.42;ReadPosRankSum=-1.043;normal_af=0.98;normal_ac=49;normal_dp=50 GT:AD:DP:GQ:PL 1/1:6,143:149:99:4054,285,0 1/1:1,178:179:99:4965,502,0 -chr1 1886500 . GCGGCTC G 2869.15 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=1.76;ClippingRankSum=-0.672;DP=69;FS=0;MLEAC=3;MLEAF=0.75;MQ=41.96;MQ0=0;MQRankSum=-1.543;QD=6.93;ReadPosRankSum=1.552;normal_af=0;normal_ac=0;normal_dp=22 GT:AD:DP:GQ:PL 0/1:1,33:34:73:1382,0,73 1/1:1,33:34:99:1526,119,0 -chr1 1886507 . ACACCGGAAGTGC A 2869.15 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=0.611;ClippingRankSum=0.357;DP=68;FS=0;MLEAC=3;MLEAF=0.75;MQ=42.12;MQ0=0;MQRankSum=-0.611;QD=3.52;ReadPosRankSum=0.866;normal_af=0;normal_ac=0;normal_dp=21 GT:AD:DP:GQ:PL 0/1:1,33:34:73:1382,0,73 1/1:0,34:34:99:1526,119,0 +chr1 1886500 . GCGGCTC G 2869.15 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=1.76;ClippingRankSum=-0.672;DP=69;FS=0;MLEAC=3;MLEAF=0.75;MQ=41.96;MQ0=0;MQRankSum=-1.543;QD=6.93;ReadPosRankSum=1.552;normal_af=0.0;normal_ac=0;normal_dp=22 GT:AD:DP:GQ:PL 0/1:1,33:34:73:1382,0,73 1/1:1,33:34:99:1526,119,0 +chr1 1886507 . ACACCGGAAGTGC A 2869.15 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=0.611;ClippingRankSum=0.357;DP=68;FS=0;MLEAC=3;MLEAF=0.75;MQ=42.12;MQ0=0;MQRankSum=-0.611;QD=3.52;ReadPosRankSum=0.866;normal_af=0.0;normal_ac=0;normal_dp=21 GT:AD:DP:GQ:PL 0/1:1,33:34:73:1382,0,73 1/1:0,34:34:99:1526,119,0 chr1 1886859 rs3795290 C T 7356.2 PASS AC=4;AF=1;AN=4;DB;DP=243;FS=0;MLEAC=4;MLEAF=1;MQ=54.7;MQ0=0;QD=30.27;normal_af=1.0;normal_ac=37;normal_dp=37 GT:AD:DP:GQ:PL 1/1:0,120:120:99:3639,360,0 1/1:0,123:123:99:3744,369,0 chr1 1887019 rs28548017 A G 8282.2 PASS AC=4;AF=1;AN=4;DB;DP=219;FS=0;MLEAC=4;MLEAF=1;MQ=58.94;MQ0=0;QD=31.98;normal_af=1.0;normal_ac=47;normal_dp=47 GT:AD:DP:GQ:PL 1/1:0,111:111:99:4217,334,0 1/1:0,108:108:99:4092,325,0 -chr1 1887091 rs139735565 CG C 10482.2 PASS AC=4;AF=1;AN=4;DB;DP=189;FS=0;MLEAC=4;MLEAF=1;MQ=40.83;MQ0=0;QD=32.93;normal_af=0.864865;normal_ac=32;normal_dp=37 GT:AD:DP:GQ:PL 1/1:0,76:76:99:4785,352,0 1/1:0,105:105:99:5733,421,0 -chr1 1887111 rs3838975 GC G 10482.2 PASS AC=4;AF=1;AN=4;DB;DP=223;FS=0;MLEAC=4;MLEAF=1;MQ=42.69;MQ0=0;QD=29.96;normal_af=0.833333;normal_ac=30;normal_dp=36 GT:AD:DP:GQ:PL 1/1:0,104:104:99:4785,352,0 1/1:0,119:119:99:5733,421,0 +chr1 1887091 rs139735565 CG C 10482.2 PASS AC=4;AF=1;AN=4;DB;DP=189;FS=0;MLEAC=4;MLEAF=1;MQ=40.83;MQ0=0;QD=32.93;normal_af=0.8648648648648649;normal_ac=32;normal_dp=37 GT:AD:DP:GQ:PL 1/1:0,76:76:99:4785,352,0 1/1:0,105:105:99:5733,421,0 +chr1 1887111 rs3838975 GC G 10482.2 PASS AC=4;AF=1;AN=4;DB;DP=223;FS=0;MLEAC=4;MLEAF=1;MQ=42.69;MQ0=0;QD=29.96;normal_af=0.8333333333333334;normal_ac=30;normal_dp=36 GT:AD:DP:GQ:PL 1/1:0,104:104:99:4785,352,0 1/1:0,119:119:99:5733,421,0 chr1 1887245 rs28575980 G A 3276.2 PASS AC=4;AF=1;AN=4;DB;DP=89;FS=0;MLEAC=4;MLEAF=1;MQ=54.3;MQ0=0;QD=29.29;normal_af=1.0;normal_ac=17;normal_dp=17 GT:AD:DP:GQ:PL 1/1:0,32:32:96:1169,96,0 1/1:0,57:57:99:2134,172,0 chr1 1888193 rs3820011 C A 9017.2 PASS AC=4;AF=1;AN=4;BaseQRankSum=0.661;ClippingRankSum=-0.778;DB;DP=295;FS=0;MLEAC=4;MLEAF=1;MQ=58.34;MQ0=0;MQRankSum=0.004;QD=30.57;ReadPosRankSum=0.853;normal_af=1.0;normal_ac=49;normal_dp=49 GT:AD:DP:GQ:PL 1/1:0,148:148:99:4541,444,0 1/1:2,145:147:99:4503,392,0 chr1 1888330 rs28535696 C T 258.54 PASS AC=4;AF=1;AN=4;DB;DP=8;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=32.32;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:104,9,0 1/1:0,5:5:15:181,15,0 @@ -451,14 +451,14 @@ chr1 1896553 rs28625839 C T 474.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.864;Clip chr1 1897753 rs4648600 C G 741.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.34;ClippingRankSum=-1.466;DB;DP=50;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.786;QD=14.83;ReadPosRankSum=1.505;normal_af=0.6666666666666666;normal_ac=6;normal_dp=9 GT:AD:DP:GQ:PL 0/1:12,11:23:99:359,0,412 0/1:14,13:27:99:411,0,465 chr1 1899279 rs61775058 A T 153.93 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.067;ClippingRankSum=0.762;DB;DP=9;FS=0;MLEAC=2;MLEAF=0.5;MQ=51.07;MQ0=0;MQRankSum=-0.067;QD=21.99;ReadPosRankSum=-0.067;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,49 1/1:0,7:7:21:186,21,0 chr1 1899319 rs61775059 T C 105.56 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=7;FS=0;MLEAC=3;MLEAF=0.75;MQ=48.22;MQ0=0;MQRankSum=-0.736;QD=21.11;ReadPosRankSum=-0.736;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,10 1/1:0,5:5:15:135,15,0 -chr1 1900024 rs56985589 TG T 88.41 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0;ClippingRankSum=-0.741;DB;DP=10;FS=0;MLEAC=2;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=-0.633;QD=8.84;ReadPosRankSum=-0.684;normal_af=0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/1:2,1:3:25:25,0,71 0/1:4,3:7:99:101,0,135 -chr1 1900106 rs145742571 T TCTC 1937.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.403;ClippingRankSum=-1.442;DB;DP=128;FS=3.662;MLEAC=2;MLEAF=0.5;MQ=54.22;MQ0=0;MQRankSum=-1.49;QD=5.05;ReadPosRankSum=-0.416;normal_af=0.391304;normal_ac=9;normal_dp=23 GT:AD:DP:GQ:PL 0/1:30,19:49:99:684,0,1525 0/1:45,34:79:99:1291,0,2209 +chr1 1900024 rs56985589 TG T 88.41 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0;ClippingRankSum=-0.741;DB;DP=10;FS=0;MLEAC=2;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=-0.633;QD=8.84;ReadPosRankSum=-0.684;normal_af=0.0;normal_ac=0;normal_dp=2 GT:AD:DP:GQ:PL 0/1:2,1:3:25:25,0,71 0/1:4,3:7:99:101,0,135 +chr1 1900106 rs145742571 T TCTC 1937.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.403;ClippingRankSum=-1.442;DB;DP=128;FS=3.662;MLEAC=2;MLEAF=0.5;MQ=54.22;MQ0=0;MQRankSum=-1.49;QD=5.05;ReadPosRankSum=-0.416;normal_af=0.0;normal_ac=0;normal_dp=23 GT:AD:DP:GQ:PL 0/1:30,19:49:99:684,0,1525 0/1:45,34:79:99:1291,0,2209 chr1 1900232 rs16824588 T C 899.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-3.165;ClippingRankSum=1.087;DB;DP=69;FS=1.707;MLEAC=2;MLEAF=0.5;MQ=55.5;MQ0=0;MQRankSum=-0.234;QD=13.04;ReadPosRankSum=-0.21;normal_af=0.35294117647058826;normal_ac=6;normal_dp=17 GT:AD:DP:GQ:PL 0/1:19,13:32:99:363,0,588 0/1:17,20:37:99:565,0,506 chr1 1900332 rs55709963 A G 198.86 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=0;ClippingRankSum=0.365;DB;DP=10;FS=0;MLEAC=3;MLEAF=0.75;MQ=53.65;MQ0=0;MQRankSum=-1.036;QD=19.89;ReadPosRankSum=-0.741;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,3:3:9:126,9,0 0/1:4,3:7:99:102,0,271 chr1 1900339 rs56126097 A G 198.86 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=-0.922;ClippingRankSum=-0.421;DB;DP=8;FS=0;MLEAC=3;MLEAF=0.75;MQ=51.94;MQ0=0;MQRankSum=-0.922;QD=24.86;ReadPosRankSum=-0.421;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 1/1:0,2:2:9:126,9,0 0/1:4,2:6:99:102,0,271 chr1 1903303 rs4648603 C T 164.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.202;ClippingRankSum=-0.201;DB;DP=14;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-1.792;QD=11.75;ReadPosRankSum=-0.421;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/1:1,2:3:31:57,0,31 0/1:6,5:11:99:136,0,190 chr1 1903712 rs13303201 C A 229.48 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.365;ClippingRankSum=0.715;DB;DP=14;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-1.892;QD=16.39;ReadPosRankSum=-1.222;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 0/1:1,5:6:19:169,0,19 0/1:5,3:8:89:89,0,154 -chr1 1908309 rs200761729 C CAG 50.78 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=12.7;ReadPosRankSum=-1.026;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,92 1/1:0,2:2:6:90,6,0 +chr1 1908309 rs200761729 C CAG 50.78 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0;MLEAC=2;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=12.7;ReadPosRankSum=-1.026;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,92 1/1:0,2:2:6:90,6,0 chr1 1909843 rs28433557 C T 96.52 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=24.13;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:86,9,0 1/1:0,1:1:3:36,3,0 chr1 1909854 rs28448395 G A 61.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=20.57;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 ./.:.:.:.:. chr1 1909868 rs28539219 G A 62.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=20.9;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 ./.:.:.:.:. @@ -469,7 +469,7 @@ chr1 1918488 rs4350140 A G 2288.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=5.728;Clip chr1 1918535 rs4535948 A T 1436.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-4.016;ClippingRankSum=-0.468;DB;DP=86;FS=10.491;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=1.483;QD=16.7;ReadPosRankSum=0.165;normal_af=0.47058823529411764;normal_ac=8;normal_dp=17 GT:AD:DP:GQ:PL 0/1:13,24:37:99:761,0,395 0/1:26,23:49:99:704,0,741 chr1 1918584 rs4603072 C T 785.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-4.962;ClippingRankSum=0.72;DB;DP=40;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.53;QD=19.64;ReadPosRankSum=2.542;normal_af=0.5;normal_ac=4;normal_dp=8 GT:AD:DP:GQ:PL 0/1:6,10:16:99:368,0,290 0/1:12,12:24:99:446,0,690 chr1 1918595 rs4466593 G A 785.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.941;ClippingRankSum=-0.376;DB;DP=28;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.612;QD=28.05;ReadPosRankSum=1.74;normal_af=0.6666666666666666;normal_ac=4;normal_dp=6 GT:AD:DP:GQ:PL 0/1:3,7:10:99:368,0,290 0/1:8,10:18:99:446,0,690 -chr1 1920434 . T TA 202.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.157;ClippingRankSum=-0.835;DP=130;FS=14.062;MLEAC=2;MLEAF=0.5;MQ=60.06;MQ0=0;MQRankSum=1.037;QD=1.56;ReadPosRankSum=-0.541;normal_af=0.0769231;normal_ac=2;normal_dp=26 GT:AD:DP:GQ:PL 0/1:27,15:42:99:185,0,359 0/1:21,16:37:99:235,0,274 +chr1 1920434 . T TA 202.4 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.157;ClippingRankSum=-0.835;DP=130;FS=14.062;MLEAC=2;MLEAF=0.5;MQ=60.06;MQ0=0;MQRankSum=1.037;QD=1.56;ReadPosRankSum=-0.541;normal_af=0.07692307692307693;normal_ac=2;normal_dp=26 GT:AD:DP:GQ:PL 0/1:27,15:42:99:185,0,359 0/1:21,16:37:99:235,0,274 chr1 1922303 rs13303195 C T 2233.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.767;ClippingRankSum=0.072;DB;DP=162;FS=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.032;QD=13.79;ReadPosRankSum=0.925;normal_af=0.5714285714285714;normal_ac=16;normal_dp=28 GT:AD:DP:GQ:PL 0/1:39,41:80:99:1115,0,977 0/1:37,45:82:99:1147,0,988 chr1 1922652 rs13303233 T C 95.41 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-0.55;ClippingRankSum=-1.754;DB;DP=7;FS=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=0;QD=15.9;ReadPosRankSum=0.937;normal_af=0.6;normal_ac=3;normal_dp=5 GT:AD:DP:GQ:PL 0/1:2,4:6:54:123,0,54 0/0:1,0:1:3:0,3,36 chr1 1923306 rs6605078 A G 46.17 PASS AC=2;AF=1;AN=2;DB;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=23.08;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:72,6,0 @@ -479,7 +479,7 @@ chr1 1941828 rs13303071 T C 153.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEA chr1 1941833 rs199857968 A G 153.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=47.12;MQ0=0;QD=27.91;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 ./.:.:.:.:. chr1 1941834 rs76020376 T A 153.46 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=47.12;MQ0=0;QD=31.88;normal_af=1.0;normal_ac=2;normal_dp=2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 ./.:.:.:.:. chr1 1941929 rs6656398 G A 115.52 PASS AC=4;AF=1;AN=4;DB;DP=4;FS=0;MLEAC=4;MLEAF=1;MQ=47.12;MQ0=0;QD=28.88;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 1/1:0,1:1:3:38,3,0 -chr1 1942713 . T TTC 55.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=65.19;MQ0=0;QD=13.78;normal_af=0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:90,6,0 +chr1 1942713 . T TTC 55.13 PASS AC=2;AF=1;AN=2;DP=2;FS=0;MLEAC=2;MLEAF=1;MQ=65.19;MQ0=0;QD=13.78;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,2:2:6:90,6,0 chr1 1948400 rs13303344 C A 55.71 PASS AC=2;AF=1;AN=2;DB;DP=3;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=18.57;normal_af=0.0;normal_ac=0;normal_dp=0 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,3:3:9:82,9,0 chr1 1952605 rs28502222 T C 178.33 PASS AC=2;AF=1;AN=2;DB;DP=5;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=30.02;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,5:5:15:205,15,0 ./.:.:.:.:. chr1 1952610 rs28407473 T C 178.33 PASS AC=2;AF=1;AN=2;DB;DP=4;FS=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=33.6;normal_af=1.0;normal_ac=1;normal_dp=1 GT:AD:DP:GQ:PL 1/1:0,4:4:15:205,15,0 ./.:.:.:.:. diff --git a/vafator/tests/resources/results/test1_output.vcf b/vafator/tests/resources/results/test1_output.vcf index 3c56812..2d06f0a 100644 --- a/vafator/tests/resources/results/test1_output.vcf +++ b/vafator/tests/resources/results/test1_output.vcf @@ -8,7 +8,7 @@ ##contig= ##INFO= ##FORMAT= -##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.4", "date": "Tue Oct 12 21:17:59 2021", "timestamp": 1634066279.511868, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test1.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test1_output.vcf"} +##vafator_command_line={"name": "multiallelic-filter", "version": "1.0.0", "date": "Wed Nov 10 22:20:26 2021", "timestamp": 1636579226.448844, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test1.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test1_output.vcf"} ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor chr1 25734793 . C T . PASS . GT 0/1 diff --git a/vafator/tests/resources/results/test2_output.vcf b/vafator/tests/resources/results/test2_output.vcf index fb4d80f..1744fcf 100644 --- a/vafator/tests/resources/results/test2_output.vcf +++ b/vafator/tests/resources/results/test2_output.vcf @@ -8,7 +8,7 @@ ##contig= ##INFO= ##FORMAT= -##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.4", "date": "Tue Oct 12 21:17:59 2021", "timestamp": 1634066279.511868, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test2.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test2_output.vcf"} +##vafator_command_line={"name": "multiallelic-filter", "version": "1.0.0", "date": "Wed Nov 10 22:20:26 2021", "timestamp": 1636579226.448844, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test2.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test2_output.vcf"} ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor chr1 25734793 . C T . PASS . GT 0/1 diff --git a/vafator/tests/resources/results/test3_output.vcf b/vafator/tests/resources/results/test3_output.vcf index 64fdedf..c13bc20 100644 --- a/vafator/tests/resources/results/test3_output.vcf +++ b/vafator/tests/resources/results/test3_output.vcf @@ -8,7 +8,7 @@ ##contig= ##INFO= ##FORMAT= -##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.4", "date": "Tue Oct 12 21:17:59 2021", "timestamp": 1634066279.511868, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test3.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test3_output.vcf"} +##vafator_command_line={"name": "multiallelic-filter", "version": "1.0.0", "date": "Wed Nov 10 22:20:26 2021", "timestamp": 1636579226.448844, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test3.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test3_output.vcf"} ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor chr1 1234 . C T . PASS . GT 0/1 diff --git a/vafator/tests/resources/results/test4_output.vcf b/vafator/tests/resources/results/test4_output.vcf index 57d75c0..c655af8 100644 --- a/vafator/tests/resources/results/test4_output.vcf +++ b/vafator/tests/resources/results/test4_output.vcf @@ -8,7 +8,7 @@ ##contig= ##INFO= ##FORMAT= -##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.4", "date": "Tue Oct 12 21:17:59 2021", "timestamp": 1634066279.511868, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test4.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test4_output.vcf"} +##vafator_command_line={"name": "multiallelic-filter", "version": "1.0.0", "date": "Wed Nov 10 22:20:26 2021", "timestamp": 1636579226.448844, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test4.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test4_output.vcf"} ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor chr4 1235 . C A . PASS tumor_af=0.2;multiallelic=,G,0.15 GT 0/1 diff --git a/vafator/tests/resources/results/test5_output.vcf b/vafator/tests/resources/results/test5_output.vcf index 3cb5356..f8a4ed2 100644 --- a/vafator/tests/resources/results/test5_output.vcf +++ b/vafator/tests/resources/results/test5_output.vcf @@ -8,7 +8,7 @@ ##contig= ##INFO= ##FORMAT= -##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.4", "date": "Tue Oct 12 21:17:59 2021", "timestamp": 1634066279.511868, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test5.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test5_output.vcf"} +##vafator_command_line={"name": "multiallelic-filter", "version": "1.0.0", "date": "Wed Nov 10 22:20:26 2021", "timestamp": 1636579226.448844, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test5.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test5_output.vcf"} ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor chr4 1235 . C A . PASS tumor_af=0.1;multiallelic=,T,0.1 GT 0/1 diff --git a/vafator/tests/resources/results/test_annotator1_output.vcf b/vafator/tests/resources/results/test_annotator1_output.vcf index b4d4e1a..5e0ef60 100644 --- a/vafator/tests/resources/results/test_annotator1_output.vcf +++ b/vafator/tests/resources/results/test_annotator1_output.vcf @@ -8,35 +8,35 @@ ##contig= ##INFO= ##FORMAT= -##vafator_command_line={"name": "vafator", "version": "1.0.0", "date": "Wed Nov 10 17:03:09 2021", "timestamp": 1636560189.413893, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test1.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test_annotator1_output.vcf", "normal_bams": ["/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_n1.bam", "/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_t1.bam"], "tumor_bams": ["/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_n1.bam", "/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_t1.bam"], "mapping_quality_threshold": 0, "base_call_quality_threshold": 29, "prefix": "RNA"} -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= +##vafator_command_line={"name": "vafator", "version": "1.0.0", "date": "Wed Nov 10 22:30:59 2021", "timestamp": 1636579859.455694, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test1.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test_annotator1_output.vcf", "bams": "RNA_normal:/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_n1.bam,/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_t1.bam;RNA_tumor:/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_n1.bam,/home/priesgo/src/github/vafator/vafator/tests/resources/COLO_829_t1.bam", "mapping_quality_threshold": 0, "base_call_quality_threshold": 29} +##INFO= +##INFO= +##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor -chr1 25734793 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr1 37323930 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr2 1234 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr2 1235 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr3 1234 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr4 1234 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr4 1235 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr4 1236 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr5 1234 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr6 1234 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr6 1235 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 -chr6 1236 . C T . PASS RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0;RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0 GT 0/1 +chr1 25734793 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr1 37323930 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr2 1234 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr2 1235 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr3 1234 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr4 1234 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr4 1235 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr4 1236 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr5 1234 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr6 1234 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr6 1235 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 +chr6 1236 . C T . PASS RNA_normal_af_1=0.0;RNA_normal_ac_1=0;RNA_normal_dp_1=0;RNA_normal_af_2=0.0;RNA_normal_ac_2=0;RNA_normal_dp_2=0;RNA_normal_af=0.0;RNA_normal_ac=0;RNA_normal_dp=0;RNA_tumor_af_1=0.0;RNA_tumor_ac_1=0;RNA_tumor_dp_1=0;RNA_tumor_af_2=0.0;RNA_tumor_ac_2=0;RNA_tumor_dp_2=0;RNA_tumor_af=0.0;RNA_tumor_ac=0;RNA_tumor_dp=0 GT 0/1 diff --git a/vafator/tests/test_annotator.py b/vafator/tests/test_annotator.py index 31901a8..6209a1a 100755 --- a/vafator/tests/test_annotator.py +++ b/vafator/tests/test_annotator.py @@ -13,7 +13,8 @@ def test_annotator(self): output_vcf = pkg_resources.resource_filename(__name__, "resources/results/test_annotator1_output.vcf") bam1 = pkg_resources.resource_filename(__name__, "resources/COLO_829_n1.bam") bam2 = pkg_resources.resource_filename(__name__, "resources/COLO_829_t1.bam") - annotator = Annotator(input_vcf=input_file, output_vcf=output_vcf, normal_bams=[bam1], tumor_bams=[bam2]) + annotator = Annotator( + input_vcf=input_file, output_vcf=output_vcf, input_bams={"normal": [bam1], "tumor": [bam2]}) annotator.run() self.assertTrue(os.path.exists(output_vcf)) @@ -35,7 +36,7 @@ def test_annotator_with_multiple_bams(self): bam1 = pkg_resources.resource_filename(__name__, "resources/COLO_829_n1.bam") bam2 = pkg_resources.resource_filename(__name__, "resources/COLO_829_t1.bam") annotator = Annotator( - input_vcf=input_file, output_vcf=output_vcf, normal_bams=[bam1, bam2], tumor_bams=[bam1, bam2]) + input_vcf=input_file, output_vcf=output_vcf, input_bams={"normal": [bam1, bam2], "tumor": [bam1, bam2]}) annotator.run() self.assertTrue(os.path.exists(output_vcf)) @@ -63,8 +64,8 @@ def test_annotator_with_prefix(self): bam1 = pkg_resources.resource_filename(__name__, "resources/COLO_829_n1.bam") bam2 = pkg_resources.resource_filename(__name__, "resources/COLO_829_t1.bam") annotator = Annotator( - input_vcf=input_file, output_vcf=output_vcf, normal_bams=[bam1, bam2], tumor_bams=[bam1, bam2], - prefix="RNA") + input_vcf=input_file, output_vcf=output_vcf, + input_bams={"RNA_normal": [bam1, bam2], "RNA_tumor": [bam1, bam2]}) annotator.run() self.assertTrue(os.path.exists(output_vcf)) @@ -104,7 +105,7 @@ def test_nist(self): bam_file = pkg_resources.resource_filename( __name__, "resources/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.chr1_1000000_2000000.bam") - annotator = Annotator(input_vcf=input_file, output_vcf=output_vcf, normal_bams=[bam_file]) + annotator = Annotator(input_vcf=input_file, output_vcf=output_vcf, input_bams={"normal": [bam_file]}) annotator.run() self.assertTrue(os.path.exists(output_vcf)) From c24683e83559a4d2457816f42d16eda513f3aeef Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 22:56:50 +0100 Subject: [PATCH 6/7] update tests to use new more generic function for pileups metrics --- vafator/tests/test_pileups.py | 65 +++++++++++++---------------------- 1 file changed, 23 insertions(+), 42 deletions(-) diff --git a/vafator/tests/test_pileups.py b/vafator/tests/test_pileups.py index 6462e6e..54fca71 100644 --- a/vafator/tests/test_pileups.py +++ b/vafator/tests/test_pileups.py @@ -1,8 +1,7 @@ from unittest import TestCase import pkg_resources import pysam -from vafator.pileups import get_insertion_metrics, get_variant_pileup, VafatorVariant, get_snv_metrics, \ - get_deletion_metrics +from vafator.pileups import get_variant_pileup, VafatorVariant, get_metrics class TestPileups(TestCase): @@ -16,71 +15,53 @@ class TestPileups(TestCase): def test_snv_metrics(self): variant = VafatorVariant(chromosome="chr1", position=1017341, reference="G", alternative=["T"]) - self._assert_snv(variant=variant, expected_ac={'G': 5, 'T': 6}, expected_dp=11) - self._assert_snv(variant=variant, expected_ac={'G': 1, 'T': 2}, expected_dp=3, min_base_quality=40) + self._assert_metrics(variant=variant, expected_ac={'G': 5, 'T': 6}, expected_dp=11) + self._assert_metrics(variant=variant, expected_ac={'G': 1, 'T': 2}, expected_dp=3, min_base_quality=40) def test_snv_metrics_2(self): variant = VafatorVariant(chromosome="chr1", position=1018144, reference="T", alternative=["C"]) - self._assert_snv(variant=variant, expected_ac={'C': 9, 'T': 11}, expected_dp=20) - self._assert_snv(variant=variant, expected_ac={'C': 3, 'T': 4}, expected_dp=7, min_base_quality=40) - self._assert_snv(variant=variant, expected_ac={'C': 0, 'T': 0}, expected_dp=0, min_mapping_quality=65) - - def _assert_snv(self, variant: VafatorVariant, expected_ac, expected_dp, - min_base_quality=0, min_mapping_quality=0): - pileups = get_variant_pileup( - variant=variant, bam=self.bam_reader, - min_base_quality=min_base_quality, min_mapping_quality=min_mapping_quality) - ac, dp = get_snv_metrics(variant=variant, pileups=pileups) - self.assertEqual(expected_ac, ac) - self.assertEqual(expected_dp, dp) + self._assert_metrics(variant=variant, expected_ac={'C': 9, 'T': 11}, expected_dp=20) + self._assert_metrics(variant=variant, expected_ac={'C': 3, 'T': 4}, expected_dp=7, min_base_quality=40) + self._assert_metrics(variant=variant, expected_ac={'C': 0, 'T': 0}, expected_dp=0, min_mapping_quality=65) def test_insertion_metrics(self): # variant called in the VCF shows no read support (!?) variant = VafatorVariant(chromosome="chr1", position=1247578, reference="T", alternative=["TGG"]) - self._assert_insertion(variant=variant, expected_ac=0, expected_dp=3) + self._assert_metrics(variant=variant, expected_ac={'TGG': 0}, expected_dp=3) # there is one read supporting this insertion of 3 Gs variant = VafatorVariant(chromosome="chr1", position=1247578, reference="T", alternative=["TGGG"]) - self._assert_insertion(variant=variant, expected_ac=1, expected_dp=3) + self._assert_metrics(variant=variant, expected_ac={'TGGG': 1}, expected_dp=3) # this ensures that the insertion sequence is checked not only the insertion length! variant = VafatorVariant(chromosome="chr1", position=1247578, reference="T", alternative=["TGGA"]) - self._assert_insertion(variant=variant, expected_ac=0, expected_dp=3) + self._assert_metrics(variant=variant, expected_ac={'TGGA': 0}, expected_dp=3) # there is one read supporting this insertion of 4 Gs variant = VafatorVariant(chromosome="chr1", position=1247578, reference="T", alternative=["TGGGG"]) - self._assert_insertion(variant=variant, expected_ac=1, expected_dp=3) + self._assert_metrics(variant=variant, expected_ac={'TGGGG': 1}, expected_dp=3) # there is no read supporting an insertion of 5 Gs variant = VafatorVariant(chromosome="chr1", position=1247578, reference="T", alternative=["TGGGGG"]) - self._assert_insertion(variant=variant, expected_ac=0, expected_dp=3) + self._assert_metrics(variant=variant, expected_ac={'TGGGGG': 0}, expected_dp=3) def test_insertion_metrics_2(self): variant = VafatorVariant(chromosome="chr1", position=1594199, reference="C", alternative=["CT"]) - self._assert_insertion(variant=variant, expected_ac=9, expected_dp=11) - self._assert_insertion(variant=variant, expected_ac=5, expected_dp=7, min_mapping_quality=40) - self._assert_insertion(variant=variant, expected_ac=4, expected_dp=4, min_base_quality=40) - - def _assert_insertion(self, variant: VafatorVariant, expected_ac, expected_dp, - min_base_quality=0, min_mapping_quality=0): - pileups = get_variant_pileup( - variant=variant, bam=self.bam_reader, - min_base_quality=min_base_quality, min_mapping_quality=min_mapping_quality) - ac, dp = get_insertion_metrics(variant=variant, pileups=pileups) - self.assertEqual(expected_ac, ac) - self.assertEqual(expected_dp, dp) + self._assert_metrics(variant=variant, expected_ac={'CT': 9}, expected_dp=11) + self._assert_metrics(variant=variant, expected_ac={'CT': 5}, expected_dp=7, min_mapping_quality=40) + self._assert_metrics(variant=variant, expected_ac={'CT': 4}, expected_dp=4, min_base_quality=40) def test_deletion_metrics(self): variant = VafatorVariant(chromosome="chr1", position=1510035, reference="GGC", alternative=["G"]) - self._assert_deletion(variant=variant, expected_ac=12, expected_dp=13) - self._assert_deletion(variant=variant, expected_ac=0, expected_dp=0, min_mapping_quality=61) - self._assert_deletion(variant=variant, expected_ac=3, expected_dp=3, min_base_quality=40) + self._assert_metrics(variant=variant, expected_ac={'G': 12}, expected_dp=13) + self._assert_metrics(variant=variant, expected_ac={'G': 0}, expected_dp=0, min_mapping_quality=61) + self._assert_metrics(variant=variant, expected_ac={'G': 3}, expected_dp=3, min_base_quality=40) # deletions with a reference sequence not matching the reference would be matched # vafator expects correct indel calls variant = VafatorVariant(chromosome="chr1", position=1510035, reference="GCC", alternative=["G"]) - self._assert_deletion(variant=variant, expected_ac=12, expected_dp=13) + self._assert_metrics(variant=variant, expected_ac={'G': 12}, expected_dp=13) - def _assert_deletion(self, variant: VafatorVariant, expected_ac, expected_dp, - min_base_quality=0, min_mapping_quality=0): + def _assert_metrics(self, variant: VafatorVariant, expected_ac, expected_dp, + min_base_quality=0, min_mapping_quality=0): pileups = get_variant_pileup( variant=variant, bam=self.bam_reader, min_base_quality=min_base_quality, min_mapping_quality=min_mapping_quality) - ac, dp = get_deletion_metrics(variant=variant, pileups=pileups) - self.assertEqual(expected_ac, ac) - self.assertEqual(expected_dp, dp) + coverage_metrics = get_metrics(variant=variant, pileups=pileups) + self.assertEqual(expected_ac, coverage_metrics.ac) + self.assertEqual(expected_dp, coverage_metrics.dp) From a505fb284f9782ff6a6ee5e90901469a8b13bcd1 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 10 Nov 2021 23:30:41 +0100 Subject: [PATCH 7/7] update documentation and nextflow workflow --- README.md | 39 +++++++++++++++++++++++++++------------ main.nf | 1 - nextflow.config | 4 +--- nf_modules/vafator.nf | 4 +--- 4 files changed, 29 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index b480ffa..4aaa79b 100755 --- a/README.md +++ b/README.md @@ -36,19 +36,35 @@ Run as follows: ``` vafator --input-vcf /path/yo/your.vcf \ --output-vcf /path/yo/your_vafator.vcf \ ---normal-bams /path/to/your_normal.bam \ ---tumor-bams /path/to/your_primary_tumor.bam,/path/to/your_metastasis_tumor.bam +--bam normal /path/to/your_normal.bam \ +--bam primary /path/to/your_primary_tumor.bam \ +--bam metastasis /path/to/your_metastasis_tumor.bam ``` -Both tumor and normal BAMs are optional, it can annotate only with the tumor BAMs or with the normal BAMs. +This will add annotations for each of the three samples `normal`, `primary` and `metastasis`: `normal_ac`, +`normal_dp`, `normal_af`, `primary_ac`, `primary_dp`, `primary_af`, +`metastasis_ac`, `metastasis_dp` and `metastasis_af`. -If more than one BAM is provided for either the tumor or the normal then the annotations are calculated across all BAMs -and for also each of them separately (eg: `tumor_af` provides the allele frequency across all tumor BAMs, `tumor_af_1` -and `tumor_af_2` provide the allele frequency on the first and second BAM respectively). +If more than one BAM is provided for any sample then the annotations are calculated across all BAMs +and for also each of them separately (eg: `primary_af` provides the allele frequency across all primary tumor BAMs, +`primary_af_1` and `primary_af_2` provide the allele frequency on the first and second BAM respectively). -Also, a `--prefix` parameter can be used to run VAFator multiple times over the same VCF without overwriting its -annotations. For instance, first `vafator [...] --prefix primary --tumor-bams /path/to/your_primary_tumor.bam` and -then `vafator [...] --prefix metastasis --tumor-bams /path/to/your_metastasis_tumor.bam`. +``` +vafator --input-vcf /path/yo/your.vcf \ +--output-vcf /path/yo/your_vafator.vcf \ +--bam primary /path/to/your_primary_tumor_1.bam \ +--bam primary /path/to/your_primary_tumor_2.bam +``` + +Alternatively, you can use `--normal-bams` and/or `--tumor-bams` and the sample names will be predefined to `normal` +and `tumor`respectively. + +``` +vafator --input-vcf /path/yo/your.vcf \ +--output-vcf /path/yo/your_vafator.vcf \ +--normal-bams /path/to/your_normal.bam \ +--tumor-bams /path/to/your_tumor_1.bam,/path/to/your_tumor_2.bam +``` Use the parameters `--mapping-quality` and `--base-call-quality` to define the minimum quality values for each read. All reads with quality values velow these thresholds will be filtered out. @@ -77,7 +93,7 @@ VAFator is available as a Nextflow pipeline for convenience. Run as follows: ``` -nextflow run tron-bioinformatics/vafator -r 1.0.0 -profile conda --input_files /path/to/your.tsv +nextflow run tron-bioinformatics/vafator -r 1.1.0 -profile conda --input_files /path/to/your.tsv ``` where `--input_files` expects four tab-separated columns **without a header**: @@ -94,8 +110,7 @@ Optional parameters: variant at the same position is kept) * `--base_call_quality`: minimum base call quality, reads with values below will be filtered out (default: 30) * `--mapping_quality`: minimum mapping quality, reads with values below will be filtered out (default: 1) -* `--prefix`: when provided the annotations are preceded by this prefix (e.g.: _tumor_ac, _tumor_af, etc), - otherwise the annotations are named as tumor_af, normal_af, tumor_ac, normal_ac, tumor_dp and normal_d + ## Support for indels diff --git a/main.nf b/main.nf index bb417f0..d479efc 100755 --- a/main.nf +++ b/main.nf @@ -12,7 +12,6 @@ params.output = "output" params.mapping_quality = false params.base_call_quality = false params.skip_multiallelic_filter = false -params.prefix = false if (params.help) { log.info params.help_message diff --git a/nextflow.config b/nextflow.config index 3f35646..2044013 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,7 +27,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] cleanup = true conda.createTimeout = '1 h' -VERSION = '1.0.0' +VERSION = '1.1.0' manifest { name = 'TRON-Bioinformatics/vafator' @@ -62,8 +62,6 @@ Optional input: * skip_multiallelic_filter: skip the filtering of multiallelics by frequency in the tumor (only highest frequency variant at the same position is kept) * base_call_quality: minimum base call quality, reads with values below will be filtered out (default: 30) * mapping_quality: minimum mapping quality, reads with values below will be filtered out (default: 1) - * prefix: when provided the annotations are preceded by this prefix (e.g.: _tumor_ac, _tumor_af, etc), - otherwise the annotations are named as tumor_af, normal_af, tumor_ac, normal_ac, tumor_dp and normal_d Output: * Annotated VCF file diff --git a/nf_modules/vafator.nf b/nf_modules/vafator.nf index 8f75357..da6ea8d 100644 --- a/nf_modules/vafator.nf +++ b/nf_modules/vafator.nf @@ -4,7 +4,6 @@ params.output = "" params.mapping_quality = false params.base_call_quality = false params.skip_multiallelic_filter = false -params.prefix = false params.enable_conda = false @@ -27,11 +26,10 @@ process VAFATOR { tumor_bams_param = tumor_bams?.trim() ? "--tumor-bams " + tumor_bams.split(",").join(" ") : "" mq_param = params.mapping_quality ? "--mapping-quality " + params.mapping_quality : "" bq_param = params.base_call_quality ? "--base-call-quality " + params.base_call_quality : "" - prefix_param = params.prefix ? "--prefix " + params.prefix : "" """ vafator \ --input-vcf ${vcf} \ - --output-vcf ${vcf.baseName}.vaf.vcf ${normal_bams_param} ${tumor_bams_param} ${mq_param} ${bq_param} ${prefix_param} + --output-vcf ${vcf.baseName}.vaf.vcf ${normal_bams_param} ${tumor_bams_param} ${mq_param} ${bq_param} """ }