# HG changeset patch
# User yhoogstrate
# Date 1394035706 18000
# Node ID 19360b35f760c6fec7dcea38dae20b95a799bced
# Parent  bafa6c859303d90e35e259ac998f2dd46edbef94
Uploaded

diff -r bafa6c859303 -r 19360b35f760 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 11:08:17 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 11:08:26 2014 -0500
@@ -65,7 +65,7 @@
 			#for $alignment in $alignments
 				 ${alignment}
 			#end for
-			 2> stderr_1.txt
+			 2>stderr_1.txt
 			
 			#if $sort_mpileup
 			 | sort -k 1,1 -k 2,2 
@@ -83,16 +83,15 @@
 					 --min-var-freq	 $varscan_min_var_freq
 					 --min-freq-for-hom $varscan_min_freq_for_hom
 					 --p-value		  $varscan_p_value
-					$varscan_strand_filter
-					$varscan_output_vcf
-					$varscan_variants
+					 $varscan_strand_filter 
+					 $varscan_variants 
 			#end if
 			
 			#if $varscan_output_vcf
 			 --output-vcf 1 
 			#end if
 			
-			 2> stderr_2.txt 
+			 2>stderr_2.txt 
 			 > $snv_output ;
 			 
 			 echo "-------------------------[ mpileup generation ]-------------------------" ;