Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 5:637f78452b3a

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Uploaded
author yhoogstrate
date Tue, 17 Dec 2013 05:03:38 -0500
parents 473e1c58d3ae
children be221fb9cabf
files varscan2_from_bam.xml
diffstat 1 files changed, 3 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/varscan2_from_bam.xml	Tue Dec 17 05:03:29 2013 -0500
+++ b/varscan2_from_bam.xml	Tue Dec 17 05:03:38 2013 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <tool id="varscan2_from_bam" name="VarScan2 from BAM">
-	<description>VarScan2 reading a *.bam file to avoid massive I/O resourcing.</description>
+	<description>VarScan2 reading a *.bam file to avoid unncessairy I/O overhead.</description>
 	<requirements>
 		<requirement type="package" version="1.0.19">samtools-mpileup-parallel</requirement>
 		<requirement type="package" version="2.3.6">VarScan</requirement>
@@ -13,7 +13,7 @@
 			The following script is written in the "Cheetah" language:
 			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
 		-->
-		samtools mpileup -t $threads -f $reference_genome
+		samtools-mpileup-parallel mpileup -t $threads -f $reference_genome
 		#for $sample in $samples
 			 ${sample.mapped_reads}
 		#end for
@@ -35,7 +35,6 @@
 	</outputs>
 	
 	<help>
-		VarScan2.3.6 is NOT compatible with the latest versions (0.1.16 and 0.1.19) of samtools.
-		It is compatible with 0.1.6, until this is fixed please stay stick to 0.1.6.
+		VarScan2.3.6.
 	</help>
 </tool>