Mercurial > repos > jeltje > samtools_1_18_mpileup

changeset 7:0af969737b28 draft

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Uploaded
author jeltje
date Mon, 12 Jan 2015 14:55:50 -0500
parents 6757453c6af9
children 48161d4bd762
files samtools_flagstat.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_flagstat.xml	Mon Jan 12 14:54:25 2015 -0500
+++ b/samtools_flagstat.xml	Mon Jan 12 14:55:50 2015 -0500
@@ -3,7 +3,7 @@
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <description>creates mpileup for VarScan2</description>
-  <command>samtools mpileup "$input1" "$input2" > "$output1"
+  <command>samtools mpileup -q 1 "$input1" "$input2" > "$output1"
   </command>
   <inputs>
     <param name="input1" type="data" format="bam" label="BAM File" />