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vaf_filter_v1.4.pl
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vaf_filter_v1.4.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 ##
## remove tumor >= 5% cut-off for smg list, Apr 23, 2020 ##
use strict;
use warnings;
die unless @ARGV == 7;
my ($run_dir,$sn,$min_vaf_somatic,$min_coverage_t,$min_coverage_n,$indel_max_size,$f_smg_list)=@ARGV;
my $f_m=$run_dir."/merged.withmutect.vcf";
my $f_maf=$run_dir."/".$sn.".withmutect.maf";
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 $indel_max_size=100;
my %smg=();
my %m2g=();
open(OUT1,">$f_filter_out");
open(OUT2,">$f_vaf_out");
if($f_smg_list ne "" && (-e $f_smg_list))
{
foreach my $l (`cat $f_smg_list`)
{
my $ltr=$l;
chomp($ltr);
$smg{$ltr}=1;
}
}
## generate mutation to gene name table ##
foreach my $l (`cat $f_maf`)
{
my $ltr=$l;
chomp($ltr);
if($ltr=~/^Hugo/) { next; }
my @t=split("\t",$ltr);
if(defined $smg{$t[0]})
{
#print $t[0],"\t",$t[4],"\t",$t[5],"\n"; <STDIN>;
$m2g{$t[4]}{$t[5]}=$t[0];
}
}
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;
my $chr=$temp[0];
my $p=$temp[1];
$ref=$temp[3];
$var=$temp[4];
if(length($ref)>$indel_max_size || length($var)>$indel_max_size) { next; }
#if($info=~/strelka-varscan/) and strelka-mutect ##
#if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/ ##
if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/)
# if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/)
{
#print $info,"\n";
#<STDIN>;
#print $ltr,"\n";
$vaf_n=$temp[9];
$vaf_t=$temp[10];
$ref=$temp[3];
$var=$temp[4];
$r_tot=0;
#print $ref,"\t",$var,"\n";
#print $vaf_n,"\n";
#print $vaf_t,"\n";
#<STDIN>;
@temp2=split(":",$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];
#Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count)
#...where:
#ref_counts = value of FORMAT column value “TAR”
#alt_counts = value of FORMAT column value “TIR”
#ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list)
#alt_t1count = $alt_counts[0] (...likewise..)
my $rcvar=(split(",",$temp2[-2]))[0];
my $rctot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0];
my $rcref=$rctot-$rcvar;
#$rc{'C'}=(split(",",$temp2[-2]))[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);
#Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count)
#...where:
#ref_counts = value of FORMAT column value “TAR”
#alt_counts = value of FORMAT column value “TIR”
#ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list)
#alt_t1count = $alt_counts[0] (...likewise..)
my $rc2var=(split(",",$temp2[-2]))[0];
my $rc2tot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0];
my $rc2ref=$rc2tot-$rc2var;
#print $rcref,"\t",$rcvar,"\t",$rctot,"\n";
#print $rc2ref,"\t",$rc2var,"\t",$rc2tot,"\n";
#<STDIN>;
#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",$rcref,"\t",$rcref/$rctot,"\t",$rcvar,"\t",$rcvar/$rctot,"\t",$rc2ref,"\t",$rc2ref/$rc2tot,"\t",$rc2var,"\t",$rc2var/$rc2tot,"\n";
if((defined $m2g{$chr}{$p} || $m2g{$chr}{$p-1} || $m2g{$chr}{$p+1} || $rc2var/$rc2tot>=$min_vaf_somatic) && $rcvar/$rctot<=$max_vaf_germline && $rc2tot>=$min_coverage_t && $rctot>=$min_coverage_n)
{
$ltr=~s/SVTYPE=//g;
print OUT1 $ltr,"\n";
}
}
#Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) for strelka
#...where:
#ref_counts = value of FORMAT column value “TAR”
#alt_counts = value of FORMAT column value “TIR”
#ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list)
#alt_t1count = $alt_counts[0] (...likewise..)
if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/)
#if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/)
{
#print $info,"\n";
#<STDIN>;
# print $ltr,"\n";
$vaf_n=$temp[9];
$vaf_t=$temp[10];
$ref=$temp[3];
$var=$temp[4];
$r_tot=0;
# print $ref,"\t",$var,"\n";
# print $vaf_n,"\n";
# <STDIN>;
@temp2=split(":",$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];
#$rc{'A'}=(split(",",$temp2[2]))[0];
#$rc{'C'}=(split(",",$temp2[3]))[0];
#$rc{'G'}=(split(",",$temp2[6]))[0];
#$rc{'T'}=(split(",",$temp2[9]))[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];
#$rc2{'A'}=(split(",",$temp2[2]))[0];
#$rc2{'C'}=(split(",",$temp2[3]))[0];
#$rc2{'G'}=(split(",",$temp2[6]))[0];
#$rc2{'T'}=(split(",",$temp2[9]))[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((defined $m2g{$chr}{$p} || $m2g{$chr}{$p-1} || $m2g{$chr}{$p+1} || $rc2var/$r_tot2>=$min_vaf_somatic) && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage_t && $r_tot>=$min_coverage_n)
{
print OUT1 $ltr,"\n";
}
}
# called snv called by varscan and mutect, indel called varscan and strelka,
if($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=varindel-pindel/)
{
$vaf_n=$temp[9];
$vaf_t=$temp[10];
@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((defined $m2g{$chr}{$p} || $m2g{$chr}{$p-1} || $m2g{$chr}{$p+1} || $tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic) && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage_t && $ndp_var+$ndp_ref>=$min_coverage_n)
{
$ltr=~s/SVTYPE=//g;
print OUT1 $ltr,"\n";
}
}
}
}