# HG changeset patch
# User yhoogstrate
# Date 1394030365 18000
# Node ID 8d1ddd8eb2b574702067bb050f8071622dced380
# Parent  77578b1e98e495778dbf71c329c0a9941bff8716
Uploaded

diff -r 77578b1e98e4 -r 8d1ddd8eb2b5 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 09:36:09 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 09:39:25 2014 -0500
@@ -84,10 +84,11 @@
 			#end if
 			
 			 --output-vcf $varscan_output_vcf
+			 2> stderr_2.txt 
 			#if $sort_mpileup == "true"
 			 | sort -k 1,1 -k 2,2 
 			#end if
-			 2> stderr_2.txt ;
+			 > $snv_output ;
 			 
 			 echo "-------------------------[ mpileup generation ]-------------------------" ;
 			 echo "" ;