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vaf_filter_v1.1.pl
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#!/usr/bin/perl
## tumor >= 5% and normal <=1%
### pindel tumor >=10% since the vaf calculation underestimate the ref coverage ##
### add the filtering for indel length ##
use strict;
use warnings;
die unless @ARGV == 1;
my ($run_dir)=@ARGV;
my $f_m=$run_dir."/merged.withmutect.vcf";
my $f_filter_out=$run_dir."/merged.filtered.withmutect.vcf";
my $f_vaf_out=$run_dir."/merged.withmutect.vaf";
my $min_vaf_somatic=0.05;
my $min_vaf_pindel=0.1;
my $max_vaf_germline=0.02;
my $min_coverage=20;
my $indel_max_size=100;
open(OUT1,">$f_filter_out");
open(OUT2,">$f_vaf_out");
foreach my $l (`cat $f_m`)
{
my $ltr=$l;
chomp($ltr);
if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; }
else {
my @temp=split("\t",$ltr);
#my $ref=$temp[3];
#my $var=$temp[4];
my $info=$temp[7];
my @temp2;
my %rc;
my %rc2;
my $r_tot;
my $r_tot2;
my $vaf_n;
my $vaf_t;
my $ref;
my $var;
my $nt;
my $ndp_ref;
my $ndp_var;
my $tdp_ref;
my $tdp_var;
$ref=$temp[3];
$var=$temp[4];
if(length($ref)>=$indel_max_size || length($var)>=$indel_max_size) { next; }
#if($info=~/strelka-varscan/)
if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/ || $info=~/set\=pindel-sindel/)
{
#print $info,"\n";
#<STDIN>;
$vaf_n=$temp[11];
$vaf_t=$temp[12];
$ref=$temp[3];
$var=$temp[4];
$r_tot=0;
@temp2=split(":",$vaf_n);
%rc=();
#print $vaf_n,"\n";
#print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n";
#<STDIN>;
#my @temp3=split(",",$temp2[0]);
#$rc{'A'}=$temp3[0];
$rc{'A'}=(split(",",$temp2[0]))[0];
$rc{'C'}=(split(",",$temp2[1]))[0];
$rc{'G'}=(split(",",$temp2[4]))[0];
$rc{'T'}=(split(",",$temp2[7]))[0];
#print $vaf_n,"\n";
#print $vaf_t,"\n";
#<STDIN>;
foreach my $nt (keys %rc)
{
$r_tot+=$rc{$nt};
#print $rc{$nt},"\n";
}
@temp2=split(":",$vaf_t);
%rc2=();
$rc2{'A'}=(split(",",$temp2[0]))[0];
$rc2{'C'}=(split(",",$temp2[1]))[0];
$rc2{'G'}=(split(",",$temp2[4]))[0];
$rc2{'T'}=(split(",",$temp2[7]))[0];
foreach $nt (sort keys %rc2)
{
$r_tot2+=$rc2{$nt};
#print $rc2{$nt},"\n";
}
#print $ltr,"\n";
my @vars=split(",",$var);
my $rcvar=0;
my $rc2var=0;
foreach my $v (@vars)
{
$rcvar+=$rc{$v};
$rc2var+=$rc2{$v};
}
#print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n";
#<STDIN>;
print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n";
if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage)
{
print OUT1 $ltr,"\n";
}
}
elsif($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=pindel-varindel/ )
{
$vaf_n=$temp[11];
$vaf_t=$temp[12];
@temp2=split(":",$vaf_n);
#print $vaf_n,"\n";
my @ndp4=split(",",$temp2[3]);
if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); }
$ndp_ref=$ndp4[0]+$ndp4[1];
$ndp_var=$ndp4[2]+$ndp4[3];
#print $vaf_t,"\n";
@temp2=split(":",$vaf_t);
my @tdp4=split(",",$temp2[3]);
if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); }
$tdp_ref=$tdp4[0]+$tdp4[1];
$tdp_var=$tdp4[2]+$tdp4[3];
print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n";
if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage)
{
$ltr=~s/SVTYPE=//g;
print OUT1 $ltr,"\n";
}
}
elsif($info=~/set\=pindel/)
{
$vaf_t=$temp[10];
$vaf_n=$temp[9];
if(!($vaf_t=~/\:/)) { next; }
if(!($vaf_n=~/\:/)) { next; }
@temp2=split(":",$vaf_n);
my @ndp2=split(",",$temp2[1]);
$ndp_ref=$ndp2[0];
$ndp_var=$ndp2[1];
@temp2=split(":",$vaf_t);
my @tdp2=split(",",$temp2[1]);
$tdp_ref=$tdp2[0];
$tdp_var=$tdp2[1];
#print $ndp_ref,"\t",$ndp_var,"\t",$tdp_ref,"\t",$tdp_var,"\n";
#<STDIN>;
print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n";
if($tdp_var/($tdp_var+$tdp_ref)>=$min_vaf_pindel && $ndp_var/($ndp_ref+$ndp_var)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage)
{
#print $ltr,"\n";
$ltr=~s/SVTYPE=//g;
print OUT1 $ltr,"\n";
}
}
}
}