diff --git a/aidiva/helper_modules/combine_expanded_indels_and_create_csv.py b/aidiva/helper_modules/combine_expanded_indels_and_create_csv.py
index 2bce651..a9d74d4 100644
--- a/aidiva/helper_modules/combine_expanded_indels_and_create_csv.py
+++ b/aidiva/helper_modules/combine_expanded_indels_and_create_csv.py
@@ -5,6 +5,10 @@
 import argparse
 from functools import partial
 from operator import itemgetter
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 def annotate_indels_with_combined_snps_information(row, grouped_expanded_vcf, feature):
diff --git a/aidiva/helper_modules/convert_indels_to_snps_and_create_vcf.py b/aidiva/helper_modules/convert_indels_to_snps_and_create_vcf.py
index 82c9a02..fc74449 100644
--- a/aidiva/helper_modules/convert_indels_to_snps_and_create_vcf.py
+++ b/aidiva/helper_modules/convert_indels_to_snps_and_create_vcf.py
@@ -3,6 +3,10 @@
 import argparse
 import random
 from Bio import SeqIO
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 def write_data_information_to_file(input_data, outfile, ref_sequence, header):
@@ -36,10 +40,10 @@ def write_data_information_to_file(input_data, outfile, ref_sequence, header):
                 elif (extended_ref_seq[i] == "G") or (extended_ref_seq[i] == "C"):
                     alt_variant = random.choice(["A", "T"])
                 elif (extended_ref_seq[i] == "N"):
-                    print("WARNING: Reference base skipped since it was N!")
+                    logger.warn("Reference base was skipped because it was 'N'!")
                     continue
                 else:
-                    print("ERROR: Something went wrong!")
+                    logger.error("The given reference sequence seems to be corrupted!")
 
                 outfile.write(str(row.CHROM).strip() + "\t" + str(window_start + i + 1).strip() + "\t" + "." + "\t" + str(extended_ref_seq[i]).strip() + "\t" + str(alt_variant).strip() + "\t" + "." + "\t" + "." + "\t" + str(row.INFO).strip() + "\n")
 
@@ -62,7 +66,7 @@ def import_vcf_data(in_data):
             continue
 
     if header_line == "":
-        print("ERROR: The VCF file seems to be corrupted")
+        logger.error("The VCF seems to be corrupted, missing header line!")
 
     # reset file pointer to begin reading at the beginning
     input_vcf.close()
diff --git a/aidiva/helper_modules/convert_vcf_to_csv.py b/aidiva/helper_modules/convert_vcf_to_csv.py
index dce8b8e..451d2c6 100644
--- a/aidiva/helper_modules/convert_vcf_to_csv.py
+++ b/aidiva/helper_modules/convert_vcf_to_csv.py
@@ -5,6 +5,7 @@
 import argparse
 from functools import partial
 from operator import itemgetter
+import logging
 
 
 variant_consequences = {"transcript_ablation": 1,
@@ -44,6 +45,8 @@
                         "feature_truncation": 35,
                         "intergenic_variant": 36}
 
+logger = logging.getLogger(__name__)
+
 
 def reformat_vcf_file_and_read_into_pandas_and_extract_header(filepath):
     header_line = ""
@@ -68,7 +71,7 @@ def reformat_vcf_file_and_read_into_pandas_and_extract_header(filepath):
             continue
 
     if header_line == "":
-        print("ERROR: The VCF file seems to be corrupted")
+        logger.warn("The VCF file seems to be corrupted")
 
     vcf_header = header_line.strip().split("\t")
     vcf_as_dataframe = pd.read_csv(tmp.name, names=vcf_header, sep="\t", comment="#", low_memory=False)
@@ -88,6 +91,18 @@ def extract_annotation_header(header):
     return annotation_header
 
 
+def extract_sample_header(header):
+    sample_header = []
+
+    for line in header:
+        if line.startswith("##SAMPLE=<"):
+            sample_entry = line.strip().replace("##SAMPLE=<", "").replace(">", "")
+            sample_id = sample_entry.split(",")[0]
+            sample_header.append(sample_id.split("=")[1])
+
+    return sample_header
+
+
 def extract_columns(cell, process_indel):
     info_fields = str(cell).split(";")
 
@@ -156,53 +171,78 @@ def extract_vep_annotation(cell, annotation_header):
     return new_cols
 
 
-def extract_sample_information(row, sample):
-    sample_header = str(row["FORMAT"]).strip().split(":")
-    sample_fields = str(row[sample + ".full"]).strip().split(":")
-
-    if len(sample_header) != len(sample_fields):
-        num_missing_entries = abs(len(sample_header) - len(sample_fields))
-        for i in range(num_missing_entries):
-            sample_fields.append(".")
+def extract_sample_information(row, sample, sample_header=None):
+    if str(row["FORMAT"]) == "MULTI":
+        if sample_header is not None:
+            sample_dict = {}
+            sample_information = []
+            for sample_entry in row[sample].split(","):
+                splitted_entry = sample_entry.split("=")
+                sample_dict[splitted_entry[0]] = splitted_entry[1]
+            
+            for sample_id in sample_header:
+                splitted_sample_information = sample_dict[sample_id].split("|")
+                if splitted_sample_information[0] == "wt":
+                    sample_information.append("0/0")
+                elif splitted_sample_information[0] == "hom":
+                    sample_information.append("1/1")
+                elif splitted_sample_information[0] == "het":
+                    sample_information.append("0/1")
+                else:
+                    logger.warning("Genotype not recognized! (%s)" % (splitted_sample_information[0]))
+
+                sample_information.append(splitted_sample_information[1])
+                sample_information.append(splitted_sample_information[2])
+                sample_information.append(sample_id + "=" + sample_dict[sample_id])
+        else:
+            logger.error("Format is MULTI but no sample_header is given!")
+    else:
+        format_entries = str(row["FORMAT"]).strip().split(":")
+        sample_fields = str(row[sample + ".full"]).strip().split(":")
 
-    if len(sample_header) != len(sample_fields):
-        num_missing_entries = abs(len(sample_header) - len(sample_fields))
-        for i in range(num_missing_entries):
-            sample_fields.append(".")
+        if len(format_entries) != len(sample_fields):
+            num_missing_entries = abs(len(format_entries) - len(sample_fields))
+            for i in range(num_missing_entries):
+                sample_fields.append(".")
 
-    if "GT" in sample_header:
-        sample_gt_information = sample_fields[sample_header.index("GT")]
-    else:
-        sample_gt_information = "./."
+        if len(format_entries) != len(sample_fields):
+            num_missing_entries = abs(len(format_entries) - len(sample_fields))
+            for i in range(num_missing_entries):
+                sample_fields.append(".")
 
-    if "DP" in sample_header:
-        sample_dp_information = sample_fields[sample_header.index("DP")]
-    else:
-        sample_dp_information = "."
+        if "GT" in format_entries:
+            sample_gt_information = sample_fields[format_entries.index("GT")]
+        else:
+            sample_gt_information = "./."
 
-    if "AD" in sample_header:
-        sample_ref_information = sample_fields[sample_header.index("AD")].split(",")[0]
-        sample_alt_information = sample_fields[sample_header.index("AD")].split(",")[1]
-    else:
-        sample_ref_information = "."
-        sample_alt_information = "."
+        if "DP" in format_entries:
+            sample_dp_information = sample_fields[format_entries.index("DP")]
+        else:
+            sample_dp_information = "."
 
-    if "GQ" in sample_header:
-        sample_gq_information = sample_fields[sample_header.index("GQ")]
-    else:
-        sample_gq_information = "."
+        if "AD" in format_entries:
+            sample_ref_information = sample_fields[format_entries.index("AD")].split(",")[0]
+            sample_alt_information = sample_fields[format_entries.index("AD")].split(",")[1]
+        else:
+            sample_ref_information = "."
+            sample_alt_information = "."
 
-    if (sample_ref_information != ".") and (sample_alt_information != "."):
-        divisor = (int(sample_ref_information) + int(sample_alt_information))
-        if divisor == 0:
-            sample_af_information = 0
+        if "GQ" in format_entries:
+            sample_gq_information = sample_fields[format_entries.index("GQ")]
         else:
-            sample_af_information = (int(sample_alt_information) / divisor)
+            sample_gq_information = "."
 
-    else:
-        sample_af_information = "."
+        if (sample_ref_information != ".") and (sample_alt_information != "."):
+            divisor = (int(sample_ref_information) + int(sample_alt_information))
+            if divisor == 0:
+                sample_af_information = 0
+            else:
+                sample_af_information = (int(sample_alt_information) / divisor)
+
+        else:
+            sample_af_information = "."
 
-    sample_information = [sample_gt_information, sample_dp_information, sample_ref_information, sample_alt_information, sample_af_information, sample_gq_information]
+        sample_information = [sample_gt_information, sample_dp_information, sample_ref_information, sample_alt_information, sample_af_information, sample_gq_information]
 
     return sample_information
 
@@ -225,12 +265,21 @@ def add_VEP_annotation_to_dataframe(annotation_header, vcf_as_dataframe):
     return vcf_as_dataframe
 
 
-def add_sample_information_to_dataframe(sample_ids, vcf_as_dataframe):
+def add_sample_information_to_dataframe(sample_ids, sample_header, vcf_as_dataframe):
     for sample in sample_ids:
-        vcf_as_dataframe.rename(columns={sample: sample + ".full"}, inplace=True)
-        sample_header = ["GT." + sample, "DP." + sample, "REF." + sample, "ALT." + sample, "AF." + sample, "GQ." + sample]
-        vcf_as_dataframe[sample_header] = vcf_as_dataframe.apply(lambda x: pd.Series(extract_sample_information(x, sample)), axis=1)
-        vcf_as_dataframe = vcf_as_dataframe.drop(columns=[sample + ".full"])
+        if (sample == "trio") or (sample == "multi"):
+            sample_header_multi = []
+            for sample_id in sample_header:
+                sample_header_multi.append("GT." + sample_id)
+                sample_header_multi.append("DP." + sample_id)
+                sample_header_multi.append("ALT." + sample_id)
+                sample_header_multi.append(sample_id + ".full")
+            vcf_as_dataframe[sample_header_multi] = vcf_as_dataframe.apply(lambda x: pd.Series(extract_sample_information(x, sample, sample_header)), axis=1)
+        else:
+            vcf_as_dataframe.rename(columns={sample: sample + ".full"}, inplace=True)
+            sample_header_default = ["GT." + sample, "DP." + sample, "REF." + sample, "ALT." + sample, "AF." + sample, "GQ." + sample]
+            vcf_as_dataframe[sample_header_default] = vcf_as_dataframe.apply(lambda x: pd.Series(extract_sample_information(x, sample)), axis=1)
+            vcf_as_dataframe = vcf_as_dataframe.drop(columns=[sample + ".full"])
 
     vcf_as_dataframe = vcf_as_dataframe.drop(columns=["FORMAT"])
 
@@ -240,6 +289,8 @@ def add_sample_information_to_dataframe(sample_ids, vcf_as_dataframe):
 def convert_vcf_to_pandas_dataframe(input_file, process_indel, num_cores):
     header, vcf_as_dataframe = reformat_vcf_file_and_read_into_pandas_and_extract_header(input_file)
 
+    logger.info("Convert")
+
     sample_ids = []
     # FORMAT column has index 8 (counted from 0) and sample columns follow afterwards (sample names are unique)
     ## TODO: add condition to check if FORMAT column exists
@@ -247,6 +298,7 @@ def convert_vcf_to_pandas_dataframe(input_file, process_indel, num_cores):
         sample_ids.append(vcf_as_dataframe.columns[i])
 
     annotation_header = extract_annotation_header(header)
+    sample_header = extract_sample_header(header)
 
     if not vcf_as_dataframe.empty:
         vcf_as_dataframe = parallelize_dataframe_processing(vcf_as_dataframe, partial(add_INFO_fields_to_dataframe, process_indel), num_cores)
@@ -254,17 +306,17 @@ def convert_vcf_to_pandas_dataframe(input_file, process_indel, num_cores):
 
         if len(vcf_as_dataframe.columns) > 8:
             if "FORMAT" in vcf_as_dataframe.columns:
-                vcf_as_dataframe = parallelize_dataframe_processing(vcf_as_dataframe, partial(add_sample_information_to_dataframe, sample_ids), num_cores)
+                vcf_as_dataframe = parallelize_dataframe_processing(vcf_as_dataframe, partial(add_sample_information_to_dataframe, sample_ids, sample_header), num_cores)
             else:
                 # This warning is always triggered when the expanded indel vcf file is processed. If it is only triggered once in this case it can be ignored.
-                print("WARNING: It seems that your VCF file does contain sample information but not FORMAT description!")
+                logger.warn("It seems that your VCF file does contain sample information but no FORMAT description!")
         else:
-            print("MISSING SAMPLE INFORMATION!")
+            logger.error("MISSING SAMPLE INFORMATION!")
 
         # replace empty strings or only spaces with NaN
         vcf_as_dataframe = vcf_as_dataframe.replace(r"^\s*$", np.nan, regex=True)
     else:
-        print("WARNING: The given VCF file is empty!")
+        logger.error("The given VCF file is empty!")
 
     return vcf_as_dataframe
 
diff --git a/aidiva/helper_modules/create_result_vcf.py b/aidiva/helper_modules/create_result_vcf.py
index 1b8e299..7c6a7be 100644
--- a/aidiva/helper_modules/create_result_vcf.py
+++ b/aidiva/helper_modules/create_result_vcf.py
@@ -1,6 +1,10 @@
 import pandas as pd
 import numpy as np
 import argparse
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 def write_header(out_file, single):
diff --git a/aidiva/helper_modules/filter_vcf.py b/aidiva/helper_modules/filter_vcf.py
index ea901d0..9efed9d 100644
--- a/aidiva/helper_modules/filter_vcf.py
+++ b/aidiva/helper_modules/filter_vcf.py
@@ -1,6 +1,7 @@
 import argparse
 import gzip
 import tempfile
+import logging
 
 
 coding_variants = ["splice_acceptor_variant",
@@ -22,6 +23,8 @@
                    "5_prime_UTR_variant",
                    "3_prime_UTR_variant"]
 
+logger = logging.getLogger(__name__)
+
 
 def filter_coding_variants(filepath, filepath_out, annotation_field_name):
     if filepath.endswith(".gz"):
@@ -62,6 +65,9 @@ def filter_coding_variants(filepath, filepath_out, annotation_field_name):
             elif line.strip().startswith("##FILTER="):
                 outfile.write(line)
                 continue
+            elif line.strip().startswith("##ANALYSISTYPE="):
+                outfile.write(line)
+                continue
             elif line.strip().startswith("##SAMPLE="):
                 outfile.write(line)
                 continue
@@ -102,7 +108,8 @@ def filter_coding_variants(filepath, filepath_out, annotation_field_name):
                 splitted_line[7] = "."
                 outfile.write("\t".join(splitted_line))
         else:
-            print("WARNING: Annotation field missing!")
+            logger.error("Annotation field missing!")
+            logger.warn("Variant filtering will be skipped!")
 
     vcf_file_to_reformat.close()
     outfile.close()
diff --git a/aidiva/helper_modules/generate_HPO_resources.py b/aidiva/helper_modules/generate_HPO_resources.py
index 8dfdbc5..410f7a4 100644
--- a/aidiva/helper_modules/generate_HPO_resources.py
+++ b/aidiva/helper_modules/generate_HPO_resources.py
@@ -91,7 +91,7 @@ def extract_hpo_graph_edges(hpo_ontology, hpo_edges_file):
 # awk -F '\t'  '{print $5}' < phenotype_annotation.tab | sort  | uniq -c | awk '{print $2 "\t" $1}' > HPO_counts.txt
 def generate_hpo_graph(hpo_counts, hpo_edges_file, hpo_graph_file):
     print("Generate HPO graph...")
-    offset =1000 # penalization for the distance
+    offset = 1000 # penalization for the distance
     # idea is a graph with attribute the IC value per node calculated
     output = hpo_graph_file # contains the nodes and edges to import in a DiGraph
 
diff --git a/aidiva/helper_modules/split_vcf_in_indel_and_snp_set.py b/aidiva/helper_modules/split_vcf_in_indel_and_snp_set.py
index b8c8469..7242f97 100644
--- a/aidiva/helper_modules/split_vcf_in_indel_and_snp_set.py
+++ b/aidiva/helper_modules/split_vcf_in_indel_and_snp_set.py
@@ -3,6 +3,10 @@
 import tempfile
 import argparse
 import gzip
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 def split_vcf_file_in_indel_and_snps_set(filepath, filepath_snp, filepath_indel):
@@ -38,8 +42,7 @@ def split_vcf_file_in_indel_and_snps_set(filepath, filepath_snp, filepath_indel)
         # remove variants with multiple alternative alleles reported
         # TODO decide how to handle them in general
         if "," in splitted_line[4]:
-            print("Variant was removed!")
-            print("REASON: Too many alternative alleles reported!")
+            logger.warn("Processed variant was removed, too many alternative alleles reported!")
             continue
         else:
             ref_length = len(splitted_line[3])
@@ -55,7 +58,7 @@ def split_vcf_file_in_indel_and_snps_set(filepath, filepath_snp, filepath_indel)
                     splitted_line[7] = splitted_line[7].replace("\n", "") + ";INDEL_ID=" + str(indel_ID)
                 outfile_indel.write("\t".join(splitted_line))
             else:
-                print("Something was not rigtht!")
+                logger.critical("Something bad happened!")
 
     vcf_file_to_reformat.close()
     outfile_snps.close()
diff --git a/aidiva/run_AIdiva.py b/aidiva/run_AIdiva.py
index 8cec98c..58d9916 100644
--- a/aidiva/run_AIdiva.py
+++ b/aidiva/run_AIdiva.py
@@ -10,6 +10,7 @@
 import variant_scoring.score_variants as predict
 import variant_prioritization.prioritize_variants as prio
 import yaml
+import logging
 
 
 if __name__=="__main__":
@@ -21,10 +22,23 @@
     parser.add_argument("--workdir", type=str, dest="workdir", metavar="workdir/", required=True, help="Path to the working directory (here all results are saved) [required]")
     parser.add_argument("--hpo_list", type=str, dest="hpo_list", metavar="hpo.txt", required=False, help="TXT file containing the HPO terms reported for the current patient")
     parser.add_argument("--gene_exclusion", type=str, dest="gene_exclusion", metavar="gene_exclusion.txt", required=False, help="Tab separated file containing the genes to exclude in the analysis. Genes are assumed to be in the first column.")
-    parser.add_argument("--family_file", type=str, dest="family_file", metavar="family.txt", required=False, help="TXT file showing the family relation of the current patient")
+    parser.add_argument("--family_file", type=str, dest="family_file", metavar="family.txt", required=False, help="TXT file showing the sample relations of the current data")
+    parser.add_argument("--family_type", type=str, dest="family_type", metavar="SINGLE", required=False, help="In case of multisample data the kind of sample relation [SINGLE, TRIO, MULTI]")
     parser.add_argument("--config", type=str, dest="config", metavar="config.yaml", required=True, help="Config file specifying the parameters for AIdiva [required]")
     parser.add_argument("--threads", type=int, dest="threads", metavar="1", required=False, help="Number of threads to use (default: 1)")
     args = parser.parse_args()
+    
+    # set up logger
+    timestamp = time.strftime("%Y%m%d-%H%M%S")
+    logging.basicConfig(filename=str(args.workdir + "/" + args.out_prefix + "_aidiva_" + timestamp + ".log"),
+                            filemode='a',
+                            format='%(asctime)s -- %(name)s - %(levelname)s - %(message)s',
+                            datefmt='%H:%M:%S',
+                            level=logging.DEBUG)
+    logger = logging.getLogger()
+    logger.info("Running AIdiva on annotated data")
+    logger.info("Start program")
+
 
     if args.threads is not None:
         num_cores = int(args.threads)
@@ -83,11 +97,11 @@
 
     # TODO: make it work if only InDel or only SNP variants are given
     if (not input_data_snp.empty) and (not input_data_indel.empty) and (not input_data_expanded_indel.empty):
-        print("Combine InDel variants ...")
+        logger.info("Combine InDel variants ...")
         input_data_combined_indel = combine_expanded_indels.parallelized_indel_combination(input_data_indel, input_data_expanded_indel, feature_list, num_cores)
 
         # predict pathogenicity score
-        print("Score variants ...")
+        logger.info("Score variants ...")
         predicted_data_snp = predict.perform_pathogenicity_score_prediction(scoring_model_snp, input_data_snp, allele_frequency_list, feature_list, num_cores)
         predicted_data_indel = predict.perform_pathogenicity_score_prediction(scoring_model_indel, input_data_combined_indel, allele_frequency_list, feature_list, num_cores)
 
@@ -97,15 +111,15 @@
         predicted_data = predicted_data[predicted_data_snp.columns]
 
         # prioritize and filter variants
-        print("Prioritize variants and finalize score ...")
+        logger.info("Prioritize variants and finalize score ...")
         prioritized_data = prio.prioritize_variants(predicted_data, hpo_resources_folder, num_cores, family_file, family_type, hpo_file, gene_exclusion_file)
 
         write_result.write_result_vcf(prioritized_data, str(working_directory + output_filename + ".vcf"), bool(family_type == "SINGLE"))
         write_result.write_result_vcf(prioritized_data[prioritized_data["FILTER_PASSED"] == 1], str(working_directory + output_filename + "_filtered.vcf"), bool(family_type == "SINGLE"))
         prioritized_data.to_csv(str(working_directory + output_filename + ".tsv"), sep="\t", index=False)
         prioritized_data[prioritized_data["FILTER_PASSED"] == 1].to_csv(str(working_directory + output_filename + "_filtered.tsv"), sep="\t", index=False)
-        print("Pipeline successfully finsished!")
+        logger.info("Pipeline successfully finsished!")
     else:
         write_result.write_result_vcf(pd.DataFrame(), str(working_directory + output_filename + ".vcf"), bool(family_type == "SINGLE"))
         write_result.write_result_vcf(pd.DataFrame(), str(working_directory + output_filename + "_filtered.vcf"), bool(family_type == "SINGLE"))
-        print("ERROR: The given input files were empty!")
+        logger.warn("The given input files were empty!")
diff --git a/aidiva/run_annotation_and_AIdiva.py b/aidiva/run_annotation_and_AIdiva.py
index 3260fd7..93b699a 100644
--- a/aidiva/run_annotation_and_AIdiva.py
+++ b/aidiva/run_annotation_and_AIdiva.py
@@ -31,6 +31,19 @@
     #parser.add_argument("--threads", type=int, dest="threads", metavar="1", required=False, help="Number of threads to use. (default: 1)")
     args = parser.parse_args()
 
+
+    # set up logger
+    timestamp = time.strftime("%Y%m%d-%H%M%S")
+    logging.basicConfig(filename=str(args.workdir + "/" + args.out_prefix + "_aidiva_" + timestamp + ".log"),
+                            filemode='a',
+                            format='%(asctime)s -- %(name)s - %(levelname)s - %(message)s',
+                            datefmt='%H:%M:%S',
+                            level=logging.DEBUG)
+    logger = logging.getLogger()
+    logger.info("Running AIdiva and annotation with VEP")
+    logger.info("Start program")
+
+
     # parse configuration file
     config_file = open(args.config, "r")
     configuration = yaml.load(config_file, Loader=yaml.SafeLoader)
@@ -92,7 +105,7 @@
 
     hpo_resources_folder = os.path.dirname(os.path.abspath(__file__)) + "/../data/hpo_resources/"
 
-    print("Starting VCF preparation...")
+    logger.info("Starting VCF preparation...")
     # sorting and filtering step to remove unsupported variants
     annotate.sort_vcf(input_vcf, str(working_directory + input_filename + "_sorted.vcf"), vep_annotation_dict)
     annotate.annotate_consequence_information(str(working_directory + input_filename + "_sorted.vcf"), str(working_directory + input_filename + "_consequence.vcf"), vep_annotation_dict, num_cores)
@@ -103,14 +116,14 @@
     expand_indels_and_create_vcf.convert_indel_vcf_to_expanded_indel_vcf(str(working_directory + input_filename + "_indel.vcf"), str(working_directory + input_filename + "_indel_expanded.vcf"), ref_path)
 
     # Annotation with VEP
-    print("Starting VEP annotation...")
+    logger.info("Starting VEP annotation...")
     annotate.call_vep_and_annotate_vcf(str(working_directory + input_filename + "_snp.vcf"), str(working_directory + input_filename + "_snp_vep.vcf"), vep_annotation_dict, False, False, num_cores)
     annotate.call_vep_and_annotate_vcf(str(working_directory + input_filename + "_indel.vcf"), str(working_directory + input_filename + "_indel_vep.vcf"), vep_annotation_dict, True, False, num_cores)
     annotate.call_vep_and_annotate_vcf(str(working_directory + input_filename + "_indel_expanded.vcf"), str(working_directory + input_filename + "_indel_expanded_vep.vcf"), vep_annotation_dict, False, True, num_cores)
 
     # Additional annotation with AnnotateFromVCF (a ngs-bits tool)
     # If VCF is used as output format VEP won't annotate from custom VCF files
-    print("Starting AnnotateFromVCF annotation...")
+    logger.info("Starting AnnotateFromVCF annotation...")
     annotate.annotate_from_vcf(str(working_directory + input_filename + "_snp_vep.vcf"), str(working_directory + input_filename + "_snp_vep_annotated.vcf"), vep_annotation_dict, num_cores)
     annotate.annotate_from_vcf(str(working_directory + input_filename + "_indel_expanded_vep.vcf"), str(working_directory + input_filename + "_indel_expanded_vep_annotated.vcf"), vep_annotation_dict, num_cores)
 
@@ -127,8 +140,7 @@
     input_data_indel_combined_annotated = combine_expanded_indels.parallelized_indel_combination(input_data_indel_annotated, input_data_indel_expanded_annotated, feature_list, num_cores)
 
     # predict pathogenicity score
-    print("Score variants...")
-    #predicted_data = predict.perform_pathogenicity_score_prediction(input_data_snp_annotated, input_data_indel_combined_annotated, scoring_model_snp, scoring_model_indel, allele_frequency_list, feature_list, num_cores)
+    logger.info("Score variants...")
     predicted_data_snp = predict.perform_pathogenicity_score_prediction(scoring_model_snp, input_data_snp_annotated, allele_frequency_list, feature_list, num_cores)
     predicted_data_indel = predict.perform_pathogenicity_score_prediction(scoring_model_indel, input_data_indel_combined_annotated, allele_frequency_list, feature_list, num_cores)
 
@@ -138,7 +150,7 @@
     predicted_data = predicted_data[predicted_data_snp.columns]
 
     # prioritize and filter variants
-    print("Filter variants and finalize score...")
+    logger.info("Filter variants and finalize score...")
     prioritized_data = prio.prioritize_variants(predicted_data, hpo_resources_folder, num_cores, family_file, family_type, hpo_file, gene_exclusion_file)
 
     ## TODO: create additional output files according to the inheritance information (only filtered data)
@@ -146,4 +158,4 @@
     write_result.write_result_vcf(prioritized_data[prioritized_data["FILTER_PASSED"] == 1], str(working_directory + input_filename + "_aidiva_result_filtered.vcf"), bool(family_type == "SINGLE"))
     prioritized_data.to_csv(str(working_directory + input_filename + "_aidiva_result.tsv"), sep="\t", index=False)
     prioritized_data[prioritized_data["FILTER_PASSED"] == 1].to_csv(str(working_directory + input_filename + "_aidiva_result_filtered.tsv"), sep="\t", index=False)
-    print("Pipeline successfully finsished!")
+    logger.info("Pipeline successfully finsished!")
diff --git a/aidiva/variant_annotation/annotate_with_vep.py b/aidiva/variant_annotation/annotate_with_vep.py
index 576ba83..12550cd 100644
--- a/aidiva/variant_annotation/annotate_with_vep.py
+++ b/aidiva/variant_annotation/annotate_with_vep.py
@@ -2,6 +2,10 @@
 import argparse
 import tempfile
 import os
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 def call_vep_and_annotate_vcf(input_vcf_file, output_vcf_file, vep_annotation_dict, basic=False, expanded=False, num_cores=1):
@@ -70,7 +74,7 @@ def call_vep_and_annotate_vcf(input_vcf_file, output_vcf_file, vep_annotation_di
     vep_command = vep_command + "--force_overwrite"
 
     subprocess.run(vep_command, shell=True, check=True)
-    print("The annotated VCF is saved as %s" % (output_vcf_file))
+    logger.info("The annotated VCF is saved as %s" % (output_vcf_file))
 
 
 def annotate_consequence_information(input_vcf_file, output_vcf_file, vep_annotation_dict, num_cores=1):
@@ -101,7 +105,7 @@ def annotate_consequence_information(input_vcf_file, output_vcf_file, vep_annota
     vep_command = vep_command + "--force_overwrite"
 
     subprocess.run(vep_command, shell=True, check=True)
-    print("The annotated VCF is saved as %s" % (output_vcf_file))
+    logger.info("The annotated VCF is saved as %s" % (output_vcf_file))
 
 
 def annotate_from_vcf(input_vcf_file, output_vcf_file, vep_annotation_dict, num_cores):
diff --git a/aidiva/variant_prioritization/get_HPO_similarity_score.py b/aidiva/variant_prioritization/get_HPO_similarity_score.py
index 19c122e..6568734 100644
--- a/aidiva/variant_prioritization/get_HPO_similarity_score.py
+++ b/aidiva/variant_prioritization/get_HPO_similarity_score.py
@@ -7,6 +7,10 @@
 import networkx as nx
 import pickle
 import numpy as np
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 # idea is :
@@ -43,7 +47,7 @@ def precompute_query_distances(HPO_graph, HPO_query):
     for hpo_term in HPO_query:
         if hpo_term not in list(HPO_graph.nodes()):
             # missing node (obsolete not updated or just wrong value)
-            print("INFO: %s not in HPO graph!" % hpo_term)
+            logger.warn("%s not in HPO graph!" % hpo_term)
             continue
 
         if str(nx.__version__).startswith("1."):
@@ -51,14 +55,14 @@ def precompute_query_distances(HPO_graph, HPO_query):
         elif str(nx.__version__).startswith("2."):
             hpo_term = HPO_graph.nodes[hpo_term].get("replaced_by", hpo_term)
         else:
-            print("ERROR: There seems to be a problem with your installation of NetworkX, make sure that you have either v1 or v2 installed!")
+            logger.error("There seems to be a problem with your installation of NetworkX, make sure that you have either v1 or v2 installed!")
 
         ## TODO: compute shortest path lengths for all nodes not only for hpo_term
         computed_distances =  nx.shortest_path_length(HPO_graph, hpo_term, weight="dist")
         
         if not HPO_query_distances:
                 HPO_query_distances = {hpo_id: float(hpo_dist) % offset for (hpo_id, hpo_dist) in computed_distances.items()}
-                print("calc whole dist")
+                logger.info("Calculate distances for HPO query")
         else:
             for hpo_id in computed_distances.keys():
                 if hpo_id in HPO_query_distances.keys():
diff --git a/aidiva/variant_prioritization/prioritize_variants.py b/aidiva/variant_prioritization/prioritize_variants.py
index c6e1257..979bfb2 100644
--- a/aidiva/variant_prioritization/prioritize_variants.py
+++ b/aidiva/variant_prioritization/prioritize_variants.py
@@ -8,6 +8,7 @@
 import re
 from functools import partial
 from itertools import combinations
+import logging
 
 if not __name__=="__main__":
     from . import get_HPO_similarity_score as gs
@@ -32,6 +33,8 @@
                    "5_prime_UTR_variant",
                    "3_prime_UTR_variant"]
 
+logger = logging.getLogger(__name__)
+
 cadd_identifier = "CADD_PHRED"
 duplication_identifier = "segmentDuplication"
 repeat_identifier = "simpleRepeat"
@@ -68,8 +71,8 @@ def prioritize_variants(variant_data, hpo_resources_folder, num_cores, family_fi
                     gene = line.rstrip().split("\t")[0].upper()
                     genes2exclude.add(gene)
         else:
-            print("The specified gene exclusion list %s is not a valid file" % (gene_exclusion_file))
-            print("No genes are excluded during filtering!")
+            logger.error("The specified gene exclusion list %s is not a valid file" % (gene_exclusion_file))
+            logger.warn("No genes will be excluded during filtering!")
 
     HPO_query = set()
     HPO_query_distances = 0
@@ -83,8 +86,8 @@ def prioritize_variants(variant_data, hpo_resources_folder, num_cores, family_fi
             HPO_query.sort() # makes sure that the gene symbols are ordered (could lead to problems otherwise)
             HPO_query_distances = gs.precompute_query_distances(HPO_graph, HPO_query)
         else:
-            print("The specified HPO list %s is not a valid file" % (hpo_list_file))
-            print("Skip HPO score finalization!")
+            logger.error("The specified HPO list %s is not a valid file" % (hpo_list_file))
+            logger.warn("HPO score finalization will be skipped!")
 
     # read family relationship (from PED file)
     family = dict()
@@ -96,14 +99,14 @@ def prioritize_variants(variant_data, hpo_resources_folder, num_cores, family_fi
                     splitline = line.split("\t")
 
                     if splitline[5] == "2":
-                       family[splitline[1]] = 1
+                        family[splitline[1]] = 1
                     elif splitline[5] == "1":
-                       family[splitline[1]] = 0
+                        family[splitline[1]] = 0
                     else:
-                       print("ERROR: There is a problem with the given PED file describing the family.")
+                        logger.error("There was a problem with the given PED file describing the family relations.")
         else:
-            print("The specified family file %s is not a valid file" % (family_file))
-            print("Skip inheritance assessment!")
+            logger.error("The specified family file %s is not a valid file" % (family_file))
+            logger.warn("Inheritance assessment will be skipped!")
 
     variant_data = parallelize_dataframe_processing(variant_data, partial(parallelized_variant_processing, family, family_type, genes2exclude, gene_2_HPO, hgnc_2_gene, gene_2_interacting, HPO_graph, HPO_query, HPO_query_distances), num_cores)
     variant_data = variant_data.sort_values(["FINAL_AIDIVA_SCORE"], ascending=[False])
@@ -157,7 +160,7 @@ def compute_hpo_relatedness_and_final_score(variant, genes2exclude, gene_2_HPO,
                 else:
                     pathogenictiy_prediction = np.nan
                 
-                print("INFO: Using dbscSNV prediction instead of AIDIVA prediction for splicing variant!")
+                logger.info("Using dbscSNV prediction instead of AIdiva prediction for splicing variant!")
 
             else:
                 pathogenictiy_prediction = float(variant["AIDIVA_SCORE"])
@@ -185,12 +188,13 @@ def compute_hpo_relatedness_and_final_score(variant, genes2exclude, gene_2_HPO,
                         gene_HPO_list = gene_2_HPO.get(gene_symbol, [])
 
                     else:
-                        print("INFO: Given gene is not covered!")
+                        logger.warn("The processed gene %s (HGNC:%s) is not found in the current HPO resources" % (variant_gene, hgnc_id))
                         gene_HPO_list = []
 
                 g_dist = gs.list_distance(HPO_graph, HPO_query, gene_HPO_list, HPO_query_distances)
                 gene_distances.append(g_dist)
 
+                # TODO: check with HGNC ID to prevent use of previous gene symbols
                 for interacting_gene in interacting_genes:
                     if (interacting_gene in genes2exclude) and (pathogenictiy_prediction < 0.8):
                         continue
@@ -199,7 +203,7 @@ def compute_hpo_relatedness_and_final_score(variant, genes2exclude, gene_2_HPO,
                         gene_HPO_list = gene_2_HPO.get(interacting_gene, [])
 
                     else:
-                        print("INFO: Given interacting gene is not covered!")
+                        logger.warn("The processed interacting gene %s is not found in the current HPO resources" % (interacting_gene))
                         gene_HPO_list = []
 
                     g_dist = gs.list_distance(HPO_graph, HPO_query, gene_HPO_list, HPO_query_distances)
@@ -237,7 +241,7 @@ def compute_hpo_relatedness_and_final_score(variant, genes2exclude, gene_2_HPO,
                     ada_score = np.nan
 
                 pathogenictiy_prediction = max([rf_score, ada_score], default=np.nan)
-                print("INFO: Using dbscSNV prediction instead of AIDIVA prediction for splicing variant!")
+                logger.info("Using dbscSNV prediction instead of AIdiva prediction for splicing variant!")
 
         else:
             pathogenictiy_prediction = float(variant["AIDIVA_SCORE"])
@@ -262,12 +266,11 @@ def check_inheritance(variant_data, family_type="SINGLE", family=None):
         variant_data = pd.concat(variant_data_grouped)
 
     elif family_type == "TRIO":
-        pass # TODO: Fix implementation of trio case and activate functionality
         if not family is None:
             variant_data["COMPOUND"] = 0
             variant_data["DOMINANT_DENOVO"] = variant_data.apply(lambda variant: check_denovo(variant, family), axis=1)
 
-            ## TODO: do we need a check for affected family members?
+            # TODO: do we need a check for affected family members?
             variant_data["DOMINANT"] = variant_data.apply(lambda variant: check_dominant(variant, family), axis=1)
             variant_data["XLINKED"] = variant_data.apply(lambda variant: check_xlinked(variant, family), axis=1)
             variant_data["RECESSIVE"] = variant_data.apply(lambda variant: check_recessive(variant, family, family_type), axis=1)
@@ -278,8 +281,8 @@ def check_inheritance(variant_data, family_type="SINGLE", family=None):
             parent_1 = ""
             parent_2 = ""
 
-            ## TODO: handle the case if affected status is given as unknown
-            ## TODO: change to be less strict and to not rely on unaffected family members
+            # TODO: handle the case if affected status is given as unknown
+            # TODO: change to be less strict and to not rely on unaffected family members
             for name in family.keys():
                 if family[name] == 1:
                     affected_child = name
@@ -291,7 +294,7 @@ def check_inheritance(variant_data, family_type="SINGLE", family=None):
                         parent_2 = name
                         continue
                     else:
-                        print("Something went wrong!")
+                        logger.error("There was a problem processing the loaded PED file")
 
             if  affected_child and parent_1 and parent_2:
                 for group in variant_data_grouped:
@@ -300,20 +303,22 @@ def check_inheritance(variant_data, family_type="SINGLE", family=None):
             variant_data = pd.concat(variant_data_grouped)
 
         else:
-            print("ERROR: If family type (TRIO) is used a proper PED file defining the family relations is required")
+            logger.error("If family type (TRIO) is used a proper PED file defining the family relations is required!")
+            logger.warn("Inheritance assessment will be skipped!")
         
-    elif (family_type == "FAMILY") and (family is not None):
-        pass # TODO: Fix implementation of family case and activate functionality
+    elif (family_type == "MULTI") and (family is not None):
         if family is not None:
             variant_data["DOMINANT"] = variant_data.apply(lambda variant: check_dominant(variant, family), axis=1)
             variant_data["XLINKED"] = variant_data.apply(lambda variant: check_xlinked(variant, family), axis=1)
             variant_data["RECESSIVE"] = variant_data.apply(lambda variant: check_recessive(variant, family, family_type), axis=1)
 
         else:
-            print("ERROR: If family type (FAMILY) is used a proper PED file defining the family relations is required")
+            logger.error("If family type (MULTI) is used a proper PED file defining the family relations (if known) is required!")
+            logger.warn("Inheritance assessment will be skipped!")
         
     else:
-        print("ERROR: Unsupported family type (%s) was given!" % family_type)
+        logger.error("Unsupported family type (%s) was given!" % family_type)
+        logger.warn("Inheritance assessment will be skipped!")
 
     variant_columns = variant_data.columns
     variant_data["INHERITANCE"] = variant_data.apply(lambda variant: add_inheritance_mode(variant, variant_columns), axis=1)
@@ -368,7 +373,7 @@ def check_filters(variant, genes2exclude, HPO_query):
     try:
         maf = float(variant["MAX_AF"])
     except Exception as e:
-        print("Allele frequency could not be identified, use 0.0 instead")
+        logger.warn("Allele frequency entry could not be identified, use 0.0 instead")
         maf = 0.0
 
     # filter for low confidence regions (these are regions where often false positives were observed)
@@ -479,8 +484,7 @@ def check_compound(gene_variants, affected_child, parent_1, parent_2):
                     gene_variants.loc[index_pair[1], "COMPOUND"] = 1
 
             if ("." in affected_child_zygosity_a) or ("." in affected_child_zygosity_b):
-                print("WARNING: Skip variant pair, uncalled genotype in affected sample!")
-
+                logger.warn("Skip variant pair, uncalled genotype in affected sample!")
 
 
 def check_compound_single(gene_variants, variant_columns):
@@ -646,7 +650,7 @@ def check_recessive(variant, family, family_type):
             continue
 
         # non-affected individuals might be hom ref, if a family is interrogated
-        elif zygosity == "0/0" and family[name] == 0 and family_type == "FAMILY":
+        elif zygosity == "0/0" and family[name] == 0 and family_type == "MULTI":
             judgement = 1
             continue
 
diff --git a/aidiva/variant_scoring/score_variants.py b/aidiva/variant_scoring/score_variants.py
index 03d29a7..47ae219 100644
--- a/aidiva/variant_scoring/score_variants.py
+++ b/aidiva/variant_scoring/score_variants.py
@@ -8,6 +8,7 @@
 import argparse
 import pickle
 from functools import partial
+import logging
 
 
 mean_dict = {"phastCons46mammal": 0.09691308336428194,
@@ -53,6 +54,8 @@
 
 random_seed = 14038
 
+logger = logging.getLogger(__name__)
+
 
 def import_model(model_file):
     model_to_import = open(model_file, "rb")
@@ -83,7 +86,7 @@ def prepare_input_data(feature_list, allele_frequency_list, input_data):
                 input_data[allele_frequency] = input_data.apply(lambda row: pd.Series(max([float(frequency) for frequency in str(row[allele_frequency]).split("&")], default=np.nan)), axis=1)
             input_data["MaxAF"] = input_data.apply(lambda row: pd.Series(max([float(frequency) for frequency in row[allele_frequency_list].tolist()])), axis=1)
         else:
-            print("ERROR: Empty allele frequency list was given!")
+            logger.error("Empty allele frequency list was given!")
 
     for feature in feature_list:
         if (feature == "MaxAF") or (feature == "MAX_AF"):
diff --git a/data/download_annotation_sources.sh b/data/download_annotation_sources.sh
new file mode 100644
index 0000000..5d8535a
--- /dev/null
+++ b/data/download_annotation_sources.sh
@@ -0,0 +1,751 @@
+#!/bin/bash
+
+folder=`pwd`
+annotation_sources=$folder/annotation_resources/
+mkdir -p $annotation_sources
+
+# Install REVEL for VEP - https://sites.google.com/site/revelgenomics/downloads
+cd $annotation_sources
+mkdir -p REVEL
+cd REVEL
+wget -c https://rothsj06.u.hpc.mssm.edu/revel/revel_all_chromosomes.csv.zip
+unzip -p revel_all_chromosomes.csv.zip | tr ',' '\t' | sed '1s/.*/#&/' | bgzip > revel_all_chromosomes.tsv.gz
+tabix -f -s 1 -b 2 -e 2 revel_all_chromosomes.tsv.gz
+
+# Install fathmm-XF for AIdiva (custom VEP annotation) - https://fathmm.biocompute.org.uk/fathmm-xf
+cd $annotation_sources
+mkdir -p fathmm-XF
+cd fathmm-XF
+wget -c http://fathmm.biocompute.org.uk/fathmm-xf/fathmm_xf_coding.vcf.gz
+python3 $folder/create_fathmm-XF_vcf.py fathmm_xf_coding.vcf.gz hg19_fathmm_xf_coding.vcf
+bgzip hg19_fathmm_xf_coding.vcf
+tabix -p vcf hg19_fathmm_xf_coding.vcf.gz
+rm fathmm_xf_coding.vcf.gz
+
+# Install ABB score for AIdiva (custom VEP annotation) - https://github.com/Francesc-Muyas/ABB
+cd $annotation_sources
+mkdir -p ABB
+cd ABB
+wget -c https://public_docs.crg.es/sossowski/publication_data/ABB/ABB_SCORE.txt
+python3 $folder/create_ABB-SCORE_bed.py ABB_SCORE.txt hg19_ABB-SCORE.bed
+bgzip hg19_ABB-SCORE.bed
+tabix -p bed hg19_ABB-SCORE.bed.gz
+rm ABB_SCORE.txt
+
+# Install Eigen phred for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p Eigen
+cd Eigen
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr1.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr2.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr3.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr4.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr5.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr6.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr7.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr8.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr9.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr10.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr11.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr12.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr13.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr14.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr15.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr16.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr17.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr18.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr19.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr20.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr21.gz
+wget -c http://web.corral.tacc.utexas.edu/WGSAdownload/resources/Eigen/Eigen_hg19_combined.tab.chr22.gz
+#python3 $folder/create_eigen_vcf.py $(ls -m *.tab.chr*.gz | tr -d '[:space:]') hg19_Eigen-phred_coding_chrom1-22.vcf
+python3 $folder/create_eigen_vcf.py $(ls -m *.tab.chr*.gz | tr -d '[:space:]') hg19_Eigen-phred_coding_chrom1-22.vcf hg19_Eigen-phred_noncoding_chrom1-22.vcf
+bgzip hg19_Eigen-phred_coding_chrom1-22.vcf
+bgzip hg19_Eigen-phred_noncoding_chrom1-22.vcf
+tabix -p vcf hg19_Eigen-phred_coding_chrom1-22.vcf.gz
+tabix -p vcf hg19_Eigen-phred_noncoding_chrom1-22.vcf.gz
+rm *.tab.chr*.gz
+
+# Install Condel for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p Condel
+cd Condel
+wget -c https://bbglab.irbbarcelona.org/fannsdb/downloads/fannsdb.tsv.gz
+python3 $folder/create_Condel_vcf.py fannsdb.tsv.gz hg19_precomputed_Condel.vcf
+bgzip hg19_precomputed_Condel.vcf
+tabix -p vcf hg19_precomputed_Condel.vcf.gz
+rm fannsdb.tsv.gz
+
+# Install MutationAssessor for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p MutationAssessor
+cd MutationAssessor
+wget -c http://mutationassessor.org/r3/MA_scores_rel3_hg19_full.tar.gz
+tar -xzf MA_scores_rel3_hg19_full.tar.gz
+python3 $folder/create_MutationAssessor_vcf.py $(ls -m MA_scores_rel3_hg19_full/*.csv | tr -d '[:space:]') hg19_precomputed_MutationAssessor_unsort.vcf
+sort -k1,1 -k2,2n hg19_precomputed_MutationAssessor_unsort.vcf > hg19_precomputed_MutationAssessor.vcf
+bgzip hg19_precomputed_MutationAssessor.vcf
+tabix -p vcf hg19_precomputed_MutationAssessor.vcf.gz
+rm MA_scores_rel3_hg19_full.tar.gz
+rm hg19_precomputed_MutationAssessor_unsort.vcf
+rm -r MA_scores_rel3_hg19_full/
+
+# Install segment duplication and simple repeats for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p UCSC
+cd UCSC
+wget -O hg19_genomicSuperDups.txt.gz ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/genomicSuperDups.txt.gz
+gunzip hg19_genomicSuperDups.txt.gz
+cut -f2,3,4,27 hg19_genomicSuperDups.txt > hg19_genomicSuperDups.bed
+grep -v "#" hg19_genomicSuperDups.bed | sort -k1,1 -k2,2n -k3,3n -t$'\t' | bgzip -c > hg19_genomicSuperDups.bed.gz
+tabix -p bed hg19_genomicSuperDups.bed.gz
+wget -O hg19_simpleRepeat.txt.gz ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/simpleRepeat.txt.gz
+gunzip hg19_simpleRepeat.txt.gz
+cut -f2,3,4,11 hg19_simpleRepeat.txt > hg19_simpleRepeat.bed
+grep -v '#' hg19_simpleRepeat.bed | sort -k1,1 -k2,2n -k3,3n -t$'\t' | bgzip -c > hg19_simpleRepeat.bed.gz
+tabix -p bed hg19_simpleRepeat.bed.gz
+
+# Install phastCons46way vertebrate for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p phastCons
+cd phastCons
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr1.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr10.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr11.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr11_gl000202_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr12.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr13.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr14.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr15.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr16.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr17.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr17_ctg5_hap1.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr17_gl000203_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr17_gl000204_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr17_gl000205_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr17_gl000206_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr18.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr18_gl000207_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr19.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr19_gl000208_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr19_gl000209_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr1_gl000191_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr1_gl000192_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr2.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr20.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr21.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr21_gl000210_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr22.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr3.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr4.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr4_ctg9_hap1.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr4_gl000193_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr4_gl000194_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr5.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_apd_hap1.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_cox_hap2.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_dbb_hap3.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_mann_hap4.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_mcf_hap5.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_qbl_hap6.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr6_ssto_hap7.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr7.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr7_gl000195_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr8.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr8_gl000196_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr8_gl000197_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr9.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr9_gl000198_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr9_gl000199_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr9_gl000200_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chr9_gl000201_random.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrM.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000211.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000212.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000213.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000214.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000215.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000216.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000217.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000218.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000219.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000220.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000221.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000222.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000223.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000224.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000225.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000226.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000227.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000228.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000229.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000230.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000231.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000232.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000233.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000234.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000235.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000236.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000237.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000238.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000239.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000240.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000241.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000242.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000243.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000244.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000245.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000246.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000247.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000248.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrUn_gl000249.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrX.phastCons46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate/chrY.phastCons46way.wigFix.gz
+wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat
+chmod +x wigToBigWig
+chmod +x bigWigCat
+gunzip *.wigFix.gz
+for f in *.wigFix; do ./wigToBigWig -fixedSummaries -keepAllChromosomes $f hg19.chrom.sizes $(basename $f ".wigFix").bw; done;
+rm *.wigFix
+./bigWigCat hg19_phastCons46way_vertebrate.bw *.phastCons46way.bw
+rm *.phastCons46way.bw
+
+# Install phastCons46way primate for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p phastCons
+cd phastCons
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr1.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr10.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr11.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr11_gl000202_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr12.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr13.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr14.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr15.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr16.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr17.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr17_ctg5_hap1.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr17_gl000203_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr17_gl000204_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr17_gl000205_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr17_gl000206_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr18.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr18_gl000207_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr19.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr19_gl000208_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr19_gl000209_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr1_gl000191_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr1_gl000192_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr2.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr20.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr21.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr21_gl000210_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr22.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr3.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr4.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr4_ctg9_hap1.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr4_gl000193_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr4_gl000194_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr5.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_apd_hap1.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_cox_hap2.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_dbb_hap3.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_mann_hap4.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_mcf_hap5.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_qbl_hap6.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr6_ssto_hap7.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr7.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr7_gl000195_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr8.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr8_gl000196_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr8_gl000197_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr9.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr9_gl000198_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr9_gl000199_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr9_gl000200_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chr9_gl000201_random.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrM.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000211.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000212.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000213.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000214.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000215.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000216.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000217.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000218.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000219.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000220.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000221.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000222.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000223.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000224.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000225.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000226.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000227.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000228.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000229.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000230.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000231.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000232.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000233.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000234.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000235.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000236.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000237.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000238.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000239.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000240.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000241.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000242.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000243.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000244.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000245.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000246.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000247.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000248.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrUn_gl000249.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrX.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates/chrY.phastCons46way.primates.wigFix.gz
+wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat
+chmod +x wigToBigWig
+chmod +x bigWigCat
+gunzip *.wigFix.gz
+for f in *.wigFix; do ./wigToBigWig -fixedSummaries -keepAllChromosomes $f hg19.chrom.sizes $(basename $f ".wigFix").bw; done;
+rm *.wigFix
+./bigWigCat hg19_phastCons46way_primate.bw *.phastCons46way.primates.bw
+rm *.phastCons46way.primates.bw
+
+# Install phastCons46way mammal for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p phastCons
+cd phastCons
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr1.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr10.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr11.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr11_gl000202_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr12.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr13.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr14.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr15.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr16.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr17.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr17_ctg5_hap1.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr17_gl000203_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr17_gl000204_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr17_gl000205_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr17_gl000206_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr18.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr18_gl000207_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr19.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr19_gl000208_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr19_gl000209_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr1_gl000191_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr1_gl000192_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr2.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr20.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr21.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr21_gl000210_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr22.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr3.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr4.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr4_ctg9_hap1.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr4_gl000193_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr4_gl000194_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr5.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_apd_hap1.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_cox_hap2.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_dbb_hap3.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_mann_hap4.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_mcf_hap5.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_qbl_hap6.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr6_ssto_hap7.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr7.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr7_gl000195_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr8.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr8_gl000196_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr8_gl000197_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr9.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr9_gl000198_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr9_gl000199_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr9_gl000200_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chr9_gl000201_random.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrM.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000211.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000212.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000213.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000214.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000215.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000216.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000217.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000218.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000219.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000220.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000221.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000222.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000223.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000224.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000225.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000226.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000227.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000228.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000229.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000230.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000231.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000232.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000233.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000234.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000235.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000236.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000237.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000238.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000239.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000240.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000241.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000242.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000243.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000244.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000245.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000246.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000247.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000248.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrUn_gl000249.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrX.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/placentalMammals/chrY.phastCons46way.placental.wigFix.gz
+wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat
+chmod +x wigToBigWig
+chmod +x bigWigCat
+gunzip *.wigFix.gz
+for f in *.wigFix; do ./wigToBigWig -fixedSummaries -keepAllChromosomes $f hg19.chrom.sizes $(basename $f ".wigFix").bw; done;
+rm *.wigFix
+./bigWigCat hg19_phastCons46way_mammal.bw *.phastCons46way.placental.bw
+rm *.phastCons46way.placental.bw
+
+# Install phyloP46way primate for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p phyloP
+cd phyloP
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr1.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr10.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr11.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr11_gl000202_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr12.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr13.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr14.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr15.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr16.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr17.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr17_ctg5_hap1.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr17_gl000203_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr17_gl000204_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr17_gl000205_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr17_gl000206_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr18.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr18_gl000207_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr19.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr19_gl000208_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr19_gl000209_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr1_gl000191_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr1_gl000192_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr2.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr20.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr21.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr21_gl000210_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr22.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr3.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr4.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr4_ctg9_hap1.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr4_gl000193_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr4_gl000194_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr5.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_apd_hap1.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_cox_hap2.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_dbb_hap3.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_mann_hap4.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_mcf_hap5.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_qbl_hap6.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr6_ssto_hap7.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr7.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr7_gl000195_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr8.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr8_gl000196_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr8_gl000197_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr9.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr9_gl000198_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr9_gl000199_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr9_gl000200_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chr9_gl000201_random.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrM.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000211.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000212.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000213.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000214.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000215.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000216.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000217.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000218.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000219.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000220.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000221.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000222.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000223.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000224.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000225.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000227.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000228.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000229.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000230.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000231.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000232.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000233.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000234.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000235.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000236.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000237.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000238.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000239.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000240.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000241.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000242.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000243.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000244.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000245.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000246.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000247.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000248.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrUn_gl000249.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrX.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/chrY.phyloP46way.primate.wigFix.gz
+wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat
+chmod +x wigToBigWig
+chmod +x bigWigCat
+gunzip *.wigFix.gz
+for f in *.wigFix; do ./wigToBigWig -fixedSummaries -keepAllChromosomes $f hg19.chrom.sizes $(basename $f ".wigFix").bw; done;
+rm *.wigFix
+./bigWigCat hg19_phyloP46way_primate.bw *.phyloP46way.primate.bw
+rm *.phyloP46way.primate.bw
+
+# Install phyloP46way mammal for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p phyloP
+cd phyloP
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr1.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr10.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr11.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr11_gl000202_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr12.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr13.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr14.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr15.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr16.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr17.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr17_ctg5_hap1.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr17_gl000203_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr17_gl000204_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr17_gl000205_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr17_gl000206_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr18.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr18_gl000207_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr19.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr19_gl000208_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr19_gl000209_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr1_gl000191_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr1_gl000192_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr2.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr20.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr21.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr21_gl000210_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr22.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr3.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr4.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr4_ctg9_hap1.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr4_gl000193_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr4_gl000194_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr5.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_apd_hap1.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_cox_hap2.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_dbb_hap3.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_mann_hap4.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_mcf_hap5.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_qbl_hap6.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr6_ssto_hap7.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr7.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr7_gl000195_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr8.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr8_gl000196_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr8_gl000197_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr9.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr9_gl000198_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr9_gl000199_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr9_gl000200_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chr9_gl000201_random.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrM.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000211.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000212.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000213.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000214.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000215.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000216.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000217.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000218.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000219.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000220.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000221.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000222.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000223.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000224.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000225.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000227.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000228.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000229.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000230.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000231.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000232.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000233.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000234.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000235.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000236.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000237.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000238.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000239.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000240.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000241.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000242.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000243.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000244.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000245.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000246.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000247.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000248.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrUn_gl000249.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrX.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/chrY.phyloP46way.placental.wigFix.gz
+wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat
+chmod +x wigToBigWig
+chmod +x bigWigCat
+gunzip *.wigFix.gz
+for f in *.wigFix; do ./wigToBigWig -fixedSummaries -keepAllChromosomes $f hg19.chrom.sizes $(basename $f ".wigFix").bw; done;
+rm *.wigFix
+./bigWigCat hg19_phyloP46way_mammal.bw *.phyloP46way.placental.bw
+rm *.phyloP46way.placental.bw
+
+# Install phyloP46way vertebrate for AIdiva (custom VEP annotation)
+cd $annotation_sources
+mkdir -p phyloP
+cd phyloP
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr1.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr10.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr11.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr11_gl000202_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr12.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr13.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr14.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr15.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr16.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr17.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr17_ctg5_hap1.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr17_gl000203_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr17_gl000204_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr17_gl000205_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr17_gl000206_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr18.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr18_gl000207_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr19.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr19_gl000208_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr19_gl000209_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr1_gl000191_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr1_gl000192_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr2.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr20.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr21.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr21_gl000210_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr22.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr3.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr4.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr4_ctg9_hap1.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr4_gl000193_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr4_gl000194_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr5.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_apd_hap1.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_cox_hap2.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_dbb_hap3.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_mann_hap4.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_mcf_hap5.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_qbl_hap6.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr6_ssto_hap7.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr7.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr7_gl000195_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr8.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr8_gl000196_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr8_gl000197_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr9.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr9_gl000198_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr9_gl000199_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr9_gl000200_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chr9_gl000201_random.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrM.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000211.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000212.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000213.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000214.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000215.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000216.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000217.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000218.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000219.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000220.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000221.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000222.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000223.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000224.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000225.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000227.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000228.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000229.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000230.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000231.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000232.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000233.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000234.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000235.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000236.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000237.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000238.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000239.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000240.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000241.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000242.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000243.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000244.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000245.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000246.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000247.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000248.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrUn_gl000249.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrX.phyloP46way.wigFix.gz
+wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/chrY.phyloP46way.wigFix.gz
+wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat
+chmod +x wigToBigWig
+chmod +x bigWigCat
+gunzip *.wigFix.gz
+for f in *.wigFix; do ./wigToBigWig -fixedSummaries -keepAllChromosomes $f hg19.chrom.sizes $(basename $f ".wigFix").bw; done;
+rm *.wigFix
+./bigWigCat hg19_phyloP46way_vertebrate.bw *.phyloP46way.bw
+rm *.phyloP46way.bw