diff --git a/variants/addgt_virmid.pl b/variants/addgt_virmid.pl index ba62bb30db7a1938178f05206f7bceb4215c8dcd..11cbf909978cb19d497e8f65edfafe56a22cf302 100755 --- a/variants/addgt_virmid.pl +++ b/variants/addgt_virmid.pl @@ -17,6 +17,15 @@ while (my $line = <VCF>) { }else { my ($chrom, $pos,$id,$ref,$alt,$score, $filter,$annot) = split(/\t/, $line); - print OUT join("\t",$line,'GT','0/0','0/1'),"\n"; + foreach $a (split(/;/,$annot)) { + my ($key,$val) = split(/=/,$a); + $hash{$key} = $val; + } + $normalgt=join(":",'0/0',$hash{NDP},$hash{NAC},$hash{NDP}-$hash{NAC}, + join(',',$hash{NDP}-$hash{NAC},$hash{NAC})); + $tumorgt=join(":",'0/0',$hash{DDP},$hash{DAC},$hash{DDP}-$hash{DAC}, + join(',',$hash{DDP}-$hash{DAC},$hash{DAC})); + print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot, + 'GT:DP:AO:RO:AD',$normalgt,$tumorgt),"\n"; } }