| Previous changeset 2:7ec666e2f315 (2015-12-21) Next changeset 4:5b63d9a21d01 (2015-12-21) |
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Commit message:
Uploaded |
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added:
phe_samtools_mpileup.sh |
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| diff -r 7ec666e2f315 -r 65b5406977c9 phe_samtools_mpileup.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phe_samtools_mpileup.sh Mon Dec 21 07:24:49 2015 -0500 |
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| @@ -0,0 +1,21 @@ +#!/bin/bash + +echo $@ + +BAM=$1 +shift +REF=$1 +shift +OUTVCF=$1 + +# TMPBAM=$$.tmpbam +# TMPBAM2=$$.tmpbam2 +# samtools view -bS $SAM > $TMPBAM +# samtools sort $TMPBAM $TMPBAM2 + +CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF" + +echo "CMD: "$CMD +eval $CMD +# rm $TMPBAM +# rm $TMPBAM2.bam |