From ec072ab9bd56a44c5daad50f9ef7df0483bd882a Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Mon, 1 Apr 2019 10:43:59 +0200
Subject: [PATCH] improve filter_multi_sample to take into account GATK
specificity
---
.../script/filter_multi_sample_vcf.py | 119 ++++++++++--------
1 file changed, 66 insertions(+), 53 deletions(-)
diff --git a/Snakemake/IMAGE_vqsr/script/filter_multi_sample_vcf.py b/Snakemake/IMAGE_vqsr/script/filter_multi_sample_vcf.py
index ad4a715..f4d410b 100755
--- a/Snakemake/IMAGE_vqsr/script/filter_multi_sample_vcf.py
+++ b/Snakemake/IMAGE_vqsr/script/filter_multi_sample_vcf.py
@@ -1,68 +1,81 @@
#!/usr/bin/env python3
-## Martijn Derks
+## Martijn Derks from Wageningen University, Netherlands and Maria Bernard from INRA, France
## Filter on average depth per sample set genotypes to missing
from collections import OrderedDict
import sys
import gzip
-import vcf
import argparse
-parser = argparse.ArgumentParser( description='Script to set genotype calls to missing if they do not contain coverage requirements')
-parser.add_argument("-v", "--vcf_file", help="VCF_file (compressed)", nargs=1)
-parser.add_argument("-b", "--bam_coverage", help="Tab delimited file with average depth per sample", nargs=1)
-parser.add_argument("-o", "--output_vcf", help="Output_VCF (gzipped)", nargs=1)
-
class FILTER_VCF:
- def avg_depth_per_sample(self, table):
- self.sample_avg_depth_dic = {}
- depth_file = open(table,"r")
- for sample in depth_file:
- sample_id, sample_avg_depth = sample.strip().split()[0], sample.split()[1]
- self.sample_avg_depth_dic[sample_id] = float(sample_avg_depth.replace('X','')) ## Dictionary with avg depth per sample
+ def avg_depth_per_sample(self, table):
+ self.sample_avg_depth_dic = {}
+ depth_file = open(table,"r")
+ for sample in depth_file:
+ sample_id, sample_avg_depth = sample.strip().split()[0], sample.split()[1]
+ self.sample_avg_depth_dic[sample_id] = float(sample_avg_depth.replace('X','')) ## Dictionary with avg depth per sample
- def filter_depth_per_sample(self, vcf, outfile):
- vcf_outfile = gzip.open(outfile,"wb")
- total_set_to_missing = 0
- nsites = 0
- with gzip.open(vcf,'r') as vcf_reader:
- for record in vcf_reader:
- filtered_call = record.strip().split("\t")
- if not record.startswith("#"):
- record = record.strip().split("\t")
- filtered_call = record[0:9]
- sample_count = 0
- nsites += 1
- for call in record[9:]:
- if not call.startswith("."):
-# if not call.startswith(".:."):
- sample = samples[sample_count]
- depth = call.split(":")[1]
- avg_depth_times_2 = float(self.sample_avg_depth_dic[sample])*2.5
- if int(depth) < 4:
- call = ".:.:."
- total_set_to_missing += 1
- if float(depth) > avg_depth_times_2: ## Set to missing if depth > avg depth*3
- call = ".:.:."
- total_set_to_missing += 1
- else:
- pass #missing
- filtered_call.append(call)
- sample_count += 1
- elif record.startswith("#CHROM"):
- samples = record.split()[9:]
- vcf_outfile.write("\t".join(filtered_call)+"\n")
- print( vcf, ": Avg set to missing per site: ", total_set_to_missing/nsites)
+ def filter_depth_per_sample(self, vcf, outfile):
+ vcf_outfile = gzip.open(outfile,"wt")
+ total_set_to_missing_un = 0
+ total_set_to_missing_low = 0
+ total_set_to_missing_high = 0
+ nsites = 0
+ format_idx = None
+ depth_idx = None
+
+ with gzip.open(vcf,'rt') as vcf_reader:
+ for record in vcf_reader:
+ filtered_call = record.strip().split("\t")
+ # variants line parsing
+ if not record.startswith("#"):
+ record = record.strip().split("\t")
+ filtered_call = record[0:9]
+ sample_count = 0
+ nsites += 1
+ # identify depth in genotype format
+ if depth_idx is None:
+ depth_idx = record[format_idx].split(":").index("DP")
+
+ # parse samples genotype calling
+ for call in record[9:]:
+ # if known
+ if not call.startswith("."):
+ sample = samples[sample_count]
+ depth = call.split(":")[depth_idx]
+ avg_depth_times_2 = float(self.sample_avg_depth_dic[sample])*2.5
+ if depth == "." :
+ call = ".:.:."
+ total_set_to_missing_un += 1
+ elif int(depth) < 4 :
+ call = ".:.:."
+ total_set_to_missing_low += 1
+ elif float(depth) > avg_depth_times_2: ## Set to missing if depth > avg depth*3
+ call = ".:.:."
+ total_set_to_missing_high += 1
+ else:
+ pass #missing
+ filtered_call.append(call)
+ sample_count += 1
+ # parsing genotype header line
+ elif record.startswith("#CHROM"):
+ samples = record.split()[9:]
+ format_idx = record.split("\t").index("FORMAT")
+
+ vcf_outfile.write("\t".join(filtered_call)+"\n")
+ print( vcf, ": Avg set to missing per site: ", (total_set_to_missing_un + total_set_to_missing_low + total_set_to_missing_high)/nsites, "unknown depth : ", total_set_to_missing_un, "low depth : ", total_set_to_missing_low, "high depth : ", total_set_to_missing_high)
if __name__=="__main__":
- F=FILTER_VCF()
- args = parser.parse_args()
- vcf = args.vcf_file[0]
- coverage_table = args.bam_coverage[0]
- out = args.output_vcf[0]
-
- F.avg_depth_per_sample(coverage_table)
- F.filter_depth_per_sample(vcf, out)
+
+ parser = argparse.ArgumentParser( description='Script to set genotype calls to missing if they do not contain coverage requirements')
+ parser.add_argument("-v", "--vcf_file", help="VCF_file (compressed)")
+ parser.add_argument("-b", "--bam_coverage", help="Tab delimited file with average depth per sample")
+ parser.add_argument("-o", "--output_vcf", help="Output_VCF (gzipped)")
+ args = parser.parse_args()
+ F=FILTER_VCF()
+
+ F.avg_depth_per_sample(args.bam_coverage)
+ F.filter_depth_per_sample(args.vcf_file, args.output_vcf)
--
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