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Snakefile.R2.smk
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Snakefile.R2.smk
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################################################################################
## DNAseq Pipeline
## Somatic variant calling with Sentieon DNAseq (from fastq files to vcf)
##
## Authors: Massimiliano Volpe, Jyotirmoy Das
## Email: [email protected], [email protected]
## Date: 11/02/2021
## Developed on behalf of the Bioinformatics Core Facility, Linköping University
##
## Rules:
## - Raw data should be stored in the same folder
## - Paths to raw data and reference must be set in the config.json file
## - Fastq filename suffix must be set in the config.json file, e.g.:
## /path_to_normal/FR1_S16_L001_R1_001.fastq.gz --> "_L001_R1_001.fastq.gz"
## /path_to_normal/FR1_S16_L001_R2_001.fastq.gz --> "_L001_R2_001.fastq.gz"
################################################################################
# Functions -------------------------------------------------------------------
def id_maker(path, sep, sample, suffix, d):
f = "".join([path, sep, sample, suffix])
# run:flowcell:lane
# l = subprocess.check_output("zcat " + f + " | head -n 1 | cut -d ':' -f 2,3,4 | sed s/:/./g | sed 's/@//'", shell=True).strip().decode()
# flowcell:lane
l = subprocess.check_output("zcat " + f + " | head -n 1 | cut -d ':' -f 3,4 | sed s/:/./g | sed 's/@//'", shell=True).strip().decode()
#d[sample] = '_'.join([sample, group, l])
d[sample] = l
return(d)
# Globals ---------------------------------------------------------------------
import subprocess
from collections import defaultdict
configfile:
"config.json"
#workdir:
# config['workdir']
R1SUFFIX = config['R1_suffix']
R2SUFFIX = config['R2_suffix']
#R3SUFFIX = config['R3_suffix']
#R4SUFFIX = config['R4_suffix']
#R5SUFFIX = config['R5_suffix']
#R6SUFFIX = config['R6_suffix']
#R7SUFFIX = config['R7_suffix']
#R8SUFFIX = config['R8_suffix']
DATA = config['dataset']
SAMPLES, = glob_wildcards(DATA + "/{sample}" + R1SUFFIX)
RESULTS = config['workdir'] + '/{sample}/'
BAMS = RESULTS + 'bams/'
LOGS = RESULTS + 'logs/'
METRICS = RESULTS + 'metrics/'
PLOTS = RESULTS + 'plots/'
MARKDUP = RESULTS + 'markdup/'
RECAL = RESULTS + 'baserecal/'
fasta = config['reference']
dbsnp = config['dbsnp']
known_Mills_indels = config['known_Mills_indels']
known_1000G_indels = config['known_1000G_indels']
#print(SAMPLES)
#d1 = defaultdict(list)
#for sample in SAMPLES:
# for file in os.listdir(config['dataset']):
# if file.startswith(sample):
# d1[sample].append(file)
#d2 = {x:sorted(d1[x]) for x in d1.keys()}
#print(d2)
# Rules -----------------------------------------------------------------------
rule all:
input:
bam = expand(BAMS + "{sample}.deduped.bam", sample=SAMPLES),
rdt = expand(RECAL + '{sample}.recal_data.table', sample=SAMPLES),
vcf = expand(RESULTS + '{sample}.dnaseq.vcf.gz', sample=SAMPLES)
#bam = expand(BAMS + "{sample}.normal_sorted.bam", sample=SAMPLES),
#normal_ml = expand(LOGS + '{sample}.normal_metrics.log', sample=SAMPLES),
rule bwa:
input:
#fq = lambda wildcards: d2[wildcards.sample],
R1 = DATA + "/{sample}" + R1SUFFIX,
R2 = DATA + "/{sample}" + R2SUFFIX,
#R3 = DATA + "/{sample}" + R3SUFFIX,
#R4 = DATA + "/{sample}" + R4SUFFIX,
#R5 = DATA + "/{sample}" + R5SUFFIX,
#R6 = DATA + "/{sample}" + R6SUFFIX,
#R7 = DATA + "/{sample}" + R7SUFFIX,
#R8 = DATA + "/{sample}" + R8SUFFIX,
ref = config['reference']
output:
sam1 = temp(BAMS + '{sample}_1.sam'),
bam1 = temp(BAMS + '{sample}_1.sorted.bam'),
#sam2 = temp(BAMS + '{sample}_2.sam'),
#bam2 = temp(BAMS + '{sample}_2.sorted.bam'),
#sam3 = temp(BAMS + '{sample}_3.sam'),
#bam3 = temp(BAMS + '{sample}_3.sorted.bam'),
#sam4 = temp(BAMS + '{sample}_4.sam'),
#bam4 = temp(BAMS + '{sample}_4.sorted.bam')
log:
bwa = LOGS + '{sample}.bwa.log',
sort = LOGS + '{sample}.sort.log'
params:
K = 10000000,
#ID = ["L001", "L002", "L003", "L004"],
ID = "L001",
SM = "{sample}",
PL = config["platform"]
threads:
48 # set the maximum number of available cores
shell:
"""
sentieon bwa mem -M -R '@RG\\tID:{params.ID[0]}\\tSM:{params.SM}\\tPL:{params.PL}' -t {threads} -K {params.K} -o {output.sam1} {input.ref} {input.R1} {input.R2} >> {log.bwa} 2>&1
sentieon util sort -r {input.ref} -i {output.sam1} -o {output.bam1} -t {threads} --sam2bam >> {log.sort} 2>&1
"""
#sentieon bwa mem -M -R '@RG\\tID:{params.ID[1]}\\tSM:{params.SM}\\tPL:{params.PL}' -t {threads} -K {params.K} -o {output.sam2} {input.ref} {input.R3} {input.R4} >> {log.bwa} 2>&1
#sentieon util sort -r {input.ref} -i {output.sam2} -o {output.bam2} -t {threads} --sam2bam >> {log.sort} 2>&1
#sentieon bwa mem -M -R '@RG\\tID:{params.ID[2]}\\tSM:{params.SM}\\tPL:{params.PL}' -t {threads} -K {params.K} -o {output.sam3} {input.ref} {input.R5} {input.R6} >> {log.bwa} 2>&1
#sentieon util sort -r {input.ref} -i {output.sam3} -o {output.bam3} -t {threads} --sam2bam >> {log.sort} 2>&1
#sentieon bwa mem -M -R '@RG\\tID:{params.ID[3]}\\tSM:{params.SM}\\tPL:{params.PL}' -t {threads} -K {params.K} -o {output.sam4} {input.ref} {input.R7} {input.R8} >> {log.bwa} 2>&1
#sentieon util sort -r {input.ref} -i {output.sam4} -o {output.bam4} -t {threads} --sam2bam >> {log.sort} 2>&1
rule markdup:
input:
bam1 = rules.bwa.output.bam1,
#bam2 = rules.bwa.output.bam2,
#bam3 = rules.bwa.output.bam3,
#bam4 = rules.bwa.output.bam4,
ref = config['reference']
output:
ns = MARKDUP + '{sample}.score.txt',
dm = MARKDUP + '{sample}.dedup_metrics.txt',
bam = BAMS + '{sample}.deduped.bam',
# cm = MARKDUP + '{sample}.coverage_metrics'
log:
LOGS + '{sample}.dedup.log'
threads:
48 # set the maximum number of available cores
shell:
# sentieon driver -r {input.ref} -t {threads} -i {output.bam} --algo CoverageMetrics {output.cm} >> {log} 2>&1
"""
sentieon driver -t {threads} -i {input.bam1} --algo LocusCollector --fun score_info {output.ns} >> {log} 2>&1
sentieon driver -t {threads} -i {input.bam1} --algo Dedup --rmdup --score_info {output.ns} --metrics {output.dm} {output.bam} >> {log} 2>&1
"""
#sentieon driver -t {threads} -i {input.bam1} -i {input.bam2} -i {input.bam3} -i {input.bam4} --algo LocusCollector --fun score_info {output.ns} >> {log} 2>&1
#sentieon driver -t {threads} -i {input.bam1} -i {input.bam2} -i {input.bam3} -i {input.bam4} --algo Dedup --rmdup --score_info {output.ns} --metrics {output.dm} {output.bam} >> {log} 2>&1
rule baserecal:
input:
bam = rules.markdup.output.bam,
ref = config['reference'],
bed = config['interval']
output:
rdt = RECAL + '{sample}.recal_data.table',
post = RECAL + '{sample}.recal_data.table.post',
recal = RECAL + '{sample}.recal.csv',
rp = PLOTS + '{sample}.recal_plots.pdf',
log:
LOGS + '{sample}.recal.log'
threads:
48 # set the maximum number of available cores
shell:
"""
sentieon driver -r {input.ref} -t {threads} -i {input.bam} --algo QualCal -k {dbsnp} -k {known_Mills_indels} -k {known_1000G_indels} {output.rdt} >> {log} 2>&1
sentieon driver --interval {input.bed} -r {input.ref} -t {threads} -i {input.bam} -q {output.rdt} --algo QualCal -k {dbsnp} -k {known_Mills_indels} -k {known_1000G_indels} {output.post} >> {log} 2>&1
sentieon driver --interval {input.bed} -t {threads} --algo QualCal --plot --before {output.rdt} --after {output.post} {output.recal} >> {log} 2>&1
sentieon plot QualCal -o {output.rp} {output.recal}
"""
rule variant_calling:
input:
bam = rules.markdup.output.bam,
ref = config['reference'],
bed = config['interval'],
rdt = rules.baserecal.output.rdt
output:
vcf = RESULTS + '{sample}.dnaseq.vcf.gz',
log:
LOGS + '{sample}.dnaseq.log'
params:
emit = 0,
call = 0,
mode = "all"
threads:
48 # set the maximum number of available cores
shell:
"""
sentieon driver --interval {input.bed} -r {input.ref} -t {threads} -i {input.bam} -q {input.rdt} --algo Haplotyper --dbsnp {dbsnp} --emit_mode={params.mode} --emit_conf={params.emit} --call_conf={params.call} {output.vcf} >> {log} 2>&1
"""
# markdup cm output is commented because output files are too big