Mercurial > repos > ulfschaefer > phe_samtools_mpileup
view phe_samtools_mpileup.sh @ 15:b13db9e677b4 draft default tip
Uploaded
author | ulfschaefer |
---|---|
date | Thu, 30 Jun 2016 03:59:23 -0400 |
parents | f78ed0f61f52 |
children |
line wrap: on
line source
#!/bin/bash echo $@ BAM=$1 shift REF=$1 shift OUTVCF=$1 CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF" echo "CMD: "$CMD eval $CMD