# HG changeset patch
# User biomonika
# Date 1407962030 14400
# Node ID f63302fe8f0c8f6c6a6fa228fca8939c9f9eb49f
# Parent  fa5992807f7ae3be8666d4097c4c3d8f7408c24b
Uploaded

diff -r fa5992807f7a -r f63302fe8f0c LINKYX_mpileup_wrapper.sh
--- a/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:11:02 2014 -0400
+++ b/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:33:50 2014 -0400
@@ -3,4 +3,5 @@
 bam_file=$2;
 reference=$3;
 
-samtools mpileup -uf $reference $2 >$results;
\ No newline at end of file
+#samtools mpileup -uf $reference $2 >$results;
+samtools mpileup -uf $reference $2 | bcftools view -p 0.85 -cgv - | vcfutils.pl varFilter >$results
\ No newline at end of file