# HG changeset patch
# User yhoogstrate
# Date 1392796003 18000
# Node ID b578aaede79b9067e7791eeef55f9be2a86cf298
# Parent  3bb39a9058d97f1b84f393edbe0817ae46776427
Uploaded

diff -r 3bb39a9058d9 -r b578aaede79b varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Tue Feb 18 11:13:41 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Feb 19 02:46:43 2014 -0500
@@ -60,7 +60,7 @@
 			#for $alignment in $alignments
 				 ${alignment}
 			#end for
-			
+			 2>/dev/null
 			 | java
 					 -Xmx64G
 					 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
@@ -79,8 +79,8 @@
 			#end if
 			
 			 --output-vcf $varscan_output_vcf
-			 
 			 > $snv_output
+			 2>&1
 		#end if
 	</command>