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Use DP4 for allele counts when AD is missing
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ckandoth committed May 1, 2019
1 parent 2d6846f commit 5453f80
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9 changes: 9 additions & 0 deletions vcf2maf.pl
Original file line number Diff line number Diff line change
Expand Up @@ -1042,6 +1042,15 @@ sub FixAlleleDepths {
$depths[0] = $fmt_info{RR};
$depths[$var_allele_idx] = $fmt_info{RV};
}
# Handle VCF lines where REF/ALT allele counts must be extracted from DP4
elsif( !defined $fmt_info{AD} and defined $fmt_info{DP4} and scalar( split( /,/, $fmt_info{DP4} )) == 4 ) {
# Reference allele depth and depths for any other ALT alleles must be left undefined
@depths = map{""} @alleles;
# DP4 is usually a comma-delimited list for ref-forward, ref-reverse, alt-forward and alt-reverse read counts
my @count = split( /,/, $fmt_info{DP4} );
$depths[0] = $count[0] + $count[1];
$depths[$var_allele_idx] = $count[2] + $count[3];
}
# Handle VCF lines from cgpPindel, where ALT depth and total depth are in PP:NP:PR:NR
elsif( !defined $fmt_info{AD} and scalar( grep{defined $fmt_info{$_}} qw/PP NP PR NR/ ) == 4 ) {
# Reference allele depth and depths for any other ALT alleles must be left undefined
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