# HG changeset patch
# User biomonika
# Date 1408028710 14400
# Node ID 48b51529b1b82ad6740164607f6c56b6defe067d
# Parent  ac995857db311b757bbb0cf9c781ba384bec2749
Uploaded

diff -r ac995857db31 -r 48b51529b1b8 LINKYX_mpileup_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_mpileup_wrapper.sh	Thu Aug 14 11:05:10 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