diff DC_Genotyper.pl @ 12:8cc26598eeac draft

Uploaded

--- a/DC_Genotyper.pl	Sat Sep 27 05:38:17 2014 -0400
+++ b/DC_Genotyper.pl	Sat Sep 27 05:49:23 2014 -0400
@@ -25,7 +25,7 @@
 ####################
 # t: target file
 # b: bam file
-# R: 2bit version of reference fasta.
+# R: reference genome files for twobit and IGV.
 # p: number of threads.
 # s: dbsnp file
 # m: minimal coverage (defaults 400x)
@@ -40,7 +40,7 @@
 if (!defined($opts{'R'})) {
 	die("Reference Genomes not specified\n");
 }
-my @refgenomes = split(",",$opts{'r'});
+my @refgenomes = split(",",$opts{'R'});
 if (!-e $refgenomes[0]) {
 	die("'$refgenomes[0]' is not a valid file path.");
 }