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Allow no-call alleles to propagate through to the MAF file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2848 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-02-16 20:46:16 +00:00
parent 217deb9809
commit f859e14cc7
1 changed files with 6 additions and 2 deletions
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8
perl/maf_annotation/vcf_to_germline_maflite.pl
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@ -22,16 +22,20 @@ while (defined($line = <STDIN>)) {
$allele1 = $ref; $allele1 = $ref;
} elsif ($geno1 eq "1") { } elsif ($geno1 eq "1") {
$allele1 = $alt; $allele1 = $alt;
} elsif ($geno1 eq ".") {
# do nothing - just leave the N in place
} else { } else {
die("only handled single alt currently:\n$line \n"); die("allele1: only handled single alt currently:\n$line \n");
} }
if ( $geno2 eq "0") { if ( $geno2 eq "0") {
$allele2 = $ref; $allele2 = $ref;
} elsif ($geno2 eq "1") { } elsif ($geno2 eq "1") {
$allele2 = $alt; $allele2 = $alt;
} elsif ($geno2 eq ".") {
# do nothing - just leave the N in place
} else { } else {
die("only handled single alt currently:\n$line\n"); die("allele2: only handled single alt currently:\n$line\n");
} }
my $ncbiBuild = "36"; my $ncbiBuild = "36";