Mercurial > repos > geert-vandeweyer > dc_genotyper

changeset 20:8262299f8f3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixed loading of dbsnp after bcftools-tabix switch.
author geert-vandeweyer
date Mon, 29 Sep 2014 07:17:11 -0400
parents 8938f339ed37
children 36e1ba3b4d1b
files DC_Genotyper.pl
diffstat 1 files changed, 7 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/DC_Genotyper.pl	Mon Sep 29 05:19:48 2014 -0400
+++ b/DC_Genotyper.pl	Mon Sep 29 07:17:11 2014 -0400
@@ -207,6 +207,13 @@
 	print SNP "chr0\t1\t.\tA\tT\n";
 	close SNP;
 }
+open IN, "$wd/dbsnp.txt";
+while (<IN>) {
+	chomp;
+	my @p = split(/\t/,$_);
+	$dbsnp{$p[0].'-'.$p[1]} = $p[3].'-'.$p[4].'-'.$p[2];
+}
+close IN;
 
 ## now process the bam file.
 mkdir "$wd/WIGS/";