# HG changeset patch
# User yhoogstrate
# Date 1394032254 18000
# Node ID cb0f5c219244d264972d85ff16df4c9be72b2e10
# Parent  d29384007de7aac614a3b8faa3244a854d2ff493
Uploaded

diff -r d29384007de7 -r cb0f5c219244 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 10:10:45 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 10:10:54 2014 -0500
@@ -66,6 +66,11 @@
 				 ${alignment}
 			#end for
 			 2> stderr_1.txt
+			
+			#if $sort_mpileup
+			 | sort -k 1,1 -k 2,2 
+			#end if
+			
 			 | java
 					 -Xmx64G
 					 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
@@ -83,14 +88,13 @@
 					$varscan_variants
 			#end if
 			
-			 --output-vcf $varscan_output_vcf
+			#if $varscan_output_vcf
+			 --output-vcf 0 
+			#else
+			 --output-vcf 0 
+			#end if
 			
 			 2> stderr_2.txt 
-			
-			#if $sort_mpileup
-			 | sort -k 1,1 -k 2,2 
-			#end if
-			
 			 > $snv_output ;
 			 
 			 echo "-------------------------[ mpileup generation ]-------------------------" ;