Mercurial > repos > ulfschaefer > phe_samtools_mpileup
comparison phe_samtools_mpileup.sh @ 0:c91df5df0faf draft
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| author | ulfschaefer |
|---|---|
| date | Mon, 21 Dec 2015 07:12:34 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:c91df5df0faf |
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| 1 #!/bin/bash | |
| 2 | |
| 3 echo $@ | |
| 4 | |
| 5 SAM=$1 | |
| 6 shift | |
| 7 REF=$1 | |
| 8 shift | |
| 9 OUTVCF=$1 | |
| 10 | |
| 11 TMPBAM=$$.tmpbam | |
| 12 TMPBAM2=$$.tmpbam2 | |
| 13 | |
| 14 samtools view -bS $SAM > $TMPBAM | |
| 15 samtools sort $TMPBAM $TMPBAM2 | |
| 16 | |
| 17 CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $TMPBAM2.bam | bcftools call -m -f GQ > $OUTVCF" | |
| 18 | |
| 19 echo "CMD: "$CMD | |
| 20 eval $CMD | |
| 21 rm $TMPBAM | |
| 22 rm $TMPBAM2.bam |