diff --git a/vcf2maf.pl b/vcf2maf.pl index 85e31a2..8d8d1d0 100644 --- a/vcf2maf.pl +++ b/vcf2maf.pl @@ -981,11 +981,12 @@ sub FixAlleleDepths { } @depths = map{( defined $fmt_info{$_.'U'} ? $fmt_info{$_.'U'} : "" )} @alleles; } - # Handle VCF Indel lines by Strelka, where variant allele depth is in TIR - elsif( !defined $fmt_info{AD} and $fmt_info{TIR} ) { - # Reference allele depth is not provided by Strelka for indels, so we have to skip it - @depths = ( "", ( split /,/, $fmt_info{TIR} )[0] ); - } + # Handle VCF Indel lines by Strelka, where variant allele depth is in TIR and reference allele depth in TAR + elsif( !defined $fmt_info{AD} and defined $fmt_info{TIR} and defined $fmt_info{TAR}) { + @depths = map{""} @alleles; + $depths[0] = ( split /,/, $fmt_info{TAR} )[0]; + $depths[$var_allele_idx] = ( split /,/, $fmt_info{TIR} )[0]; + # Handle VCF lines by CaVEMan, where allele depths are in FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ elsif( !defined $fmt_info{AD} and scalar( grep{defined $fmt_info{$_}} qw/FAZ FCZ FGZ FTZ RAZ RCZ RGZ RTZ/ ) == 8 ) { # Create tags for forward+reverse strand reads, and use those to determine REF/ALT depths