From 4965d6b26a443fb6d6cacfbceea781b652fdec34 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Mar 2010 19:08:37 +0000
Subject: [PATCH] Passing just the single alternate allele to the converted maf
 on the recommendation of mike lawrence and kiran.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3026 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../maf_annotation/vcf_to_germline_maflite.pl | 29 ++-----------------
 1 file changed, 2 insertions(+), 27 deletions(-)

diff --git a/perl/maf_annotation/vcf_to_germline_maflite.pl b/perl/maf_annotation/vcf_to_germline_maflite.pl
index e767fc71c..fadd98753 100755
--- a/perl/maf_annotation/vcf_to_germline_maflite.pl
+++ b/perl/maf_annotation/vcf_to_germline_maflite.pl
@@ -11,33 +11,8 @@ my $line;
 while (defined($line = <STDIN>)) {
     if ($line =~ /#/) { next; }
 
-    my ($chrom, $pos, $rsName, $ref, $alt, $qual, $filter, $info, $format, $sampleA) = split("\t", $line);
-
-    my ($genoNum) = split(":", $sampleA);
-    my ($geno1, $geno2) = split("/",$genoNum);
-       
-    my $allele1 = "N";
-    my $allele2 = "N";
-    if ( $geno1 eq "0") { 
-        $allele1 = $ref;
-    } elsif ($geno1 eq "1") {
-        $allele1 = $alt;
-    } elsif ($geno1 eq ".") {
-        # do nothing - just leave the N in place
-    } else {
-        die("allele1: only handled single alt currently:\n$line \n");
-    }
-
-    if ( $geno2 eq "0") { 
-        $allele2 = $ref;
-    } elsif ($geno2 eq "1") {
-        $allele2 = $alt;
-    } elsif ($geno2 eq ".") {
-        # do nothing - just leave the N in place
-    } else {
-        die("allele2: only handled single alt currently:\n$line\n");
-    }
+    my ($chrom, $pos, $rsName, $ref, $alt) = split("\t", $line);
 
     my $ncbiBuild = "36";
-    print join("\t", ($ncbiBuild, $chrom, $pos, $pos, $ref, $allele1, $allele2, $normalAlias, $normalAlias)) . "\n";
+    print join("\t", ($ncbiBuild, $chrom, $pos, $pos, $ref, $alt, $alt, $normalAlias, $normalAlias)) . "\n";
 }