Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 36:b578aaede79b

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Uploaded
author yhoogstrate
date Wed, 19 Feb 2014 02:46:43 -0500
parents 3bb39a9058d9
children 17f10d28dab3
files varscan_mpileup2snp_from_bam.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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>