58 lines
2.0 KiB
Perl
58 lines
2.0 KiB
Perl
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#!/usr/bin/perl
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use strict;
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use warnings;
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die "usage:perl $0 germline/somatic tumor_prefix name input_file outputDir" unless @ARGV==5;
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my($type,$tumor,$name,$input,$outputDir)=@ARGV;
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`filter_vep -i $input -o ${outputDir}/${name}_${type}_vepanno_filter.vcf --format vcf --force_overwrite --filter "(Consequence != synonymous_variant) and (Consequence != intron_variant) and (Consequence != intergenic_variant) and (Consequence != 3_prime_UTR_variant) and (Consequence != upstream_gene_variant) and (Consequence != downstream_gene_variant) and (Consequence != 5_prime_UTR_variant)"`;
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if($type eq "germline"){
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open IN,"${outputDir}/${name}_${type}_vepanno_filter.vcf";
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open OUT,">${outputDir}/${name}_${type}_vepanno_Filter.vcf";
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while(<IN>){
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if (/^##/){
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print OUT;
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next;
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}elsif(/^#CHROM/){
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$_=~s/TUMOR/$tumor/;
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print OUT;
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next;
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}else{
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chomp;
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my @line=split("\t",$_);
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next if $line[6] ne "PASS";
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my $n_af=(split(":",$line[-2]))[-2];
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my $t_af=(split(":",$line[-1]))[-2];
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$n_af=~s/%//;
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$t_af=~s/%//;
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print OUT "$_\n" if ($n_af>=10 and $t_af>=10);
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}
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}
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`rm ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
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`mv ${outputDir}/${name}_${type}_vepanno_Filter.vcf ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
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}elsif($type eq "somatic"){
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open IN,"${outputDir}/${name}_${type}_vepanno_filter.vcf";
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open OUT,">${outputDir}/${name}_${type}_vepanno_Filter.vcf";
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while(<IN>){
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if (/^##/){
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print OUT;
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next;
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}elsif(/^#CHROM/){
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$_=~s/TUMOR/$tumor/;
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print OUT;
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next;
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}else{
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chomp;
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my @line=split("\t",$_);
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next if $line[6] ne "PASS";
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my $n_af=(split(":",$line[-2]))[-2];
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my $t_af=(split(":",$line[-1]))[-2];
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$n_af=~s/%//;
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$t_af=~s/%//;
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print OUT "$_\n" if ($n_af<2 and $t_af>=5);
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}
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}
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`rm ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
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`mv ${outputDir}/${name}_${type}_vepanno_Filter.vcf ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
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}
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