# HG changeset patch
# User biomonika
# Date 1407962062 14400
# Node ID 6351a3faf4e3e5ac155abac70091bc1d3fb4445b
# Parent  188b16f2d6f8fdea5d0286e51069a4df58f40a8c
Uploaded

diff -r 188b16f2d6f8 -r 6351a3faf4e3 LINKYX_mpileup_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:34:22 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 $2 | bcftools view -p 0.85 -cgv - | vcfutils.pl varFilter >$results
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