# HG changeset patch
# User jeltje
# Date 1421092550 18000
# Node ID 0af969737b283cd7858939cdb34256b59f3f63ea
# Parent  6757453c6af9e0d296a41f5b739f20992732c869
Uploaded

diff -r 6757453c6af9 -r 0af969737b28 samtools_flagstat.xml
--- 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" />