# HG changeset patch
# User biomonika
# Date 1407963085 14400
# Node ID 0b2d6cee9f2e5c53388db151ac20942c8703f13c
# Parent  7f57b3213b2b85dba77cfc831bba25957922d274
Uploaded

diff -r 7f57b3213b2b -r 0b2d6cee9f2e LINKYX_mpileup_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:51:25 2014 -0400
@@ -0,0 +1,7 @@
+#!/bin/bash
+results=$1;
+bam_file=$2;
+reference=$3;
+
+#samtools mpileup -uf $reference $2 >$results;
+samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt
\ No newline at end of file