Mercurial > repos > biomonika > linkyx

diff LINKYX_mpileup_wrapper.sh @ 22:7997c93ee479

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last attempt to install perl as part of linkyx
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 19:40:01 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_mpileup_wrapper.sh	Thu Sep 11 19:40:01 2014 -0400
@@ -0,0 +1,8 @@
+#!/bin/bash
+results=$1;
+bam_file=$2;
+reference=$3;
+
+sorted_bam=${bam_file}_sorted
+
+samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results