Mercurial > repos > biomonika > linkyx

view LINKYX_mpileup_wrapper.sh @ 7:90098d9cb691 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
workflows updated
author biomonika <biomonika@psu.edu>
date Fri, 20 Feb 2015 18:34:34 -0500
parents 0d8315be76b7
children
line wrap: on
line source

#!/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