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Fixed handling of allele depths for Indels called by Strelka #215

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Mar 17, 2019
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Fixed handling of allele depths for Indels called by Strelka #215

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11 changes: 6 additions & 5 deletions vcf2maf.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -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];

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Missing a closing bracket } here. But otherwise looks good. Thanks for the PR!

# 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
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