Mercurial > repos > ulfschaefer > phe_samtools_mpileup
comparison phe_samtools_mpileup.sh @ 3:65b5406977c9 draft
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| author | ulfschaefer |
|---|---|
| date | Mon, 21 Dec 2015 07:24:49 -0500 |
| parents | |
| children | f78ed0f61f52 |
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| 2:7ec666e2f315 | 3:65b5406977c9 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 echo $@ | |
| 4 | |
| 5 BAM=$1 | |
| 6 shift | |
| 7 REF=$1 | |
| 8 shift | |
| 9 OUTVCF=$1 | |
| 10 | |
| 11 # TMPBAM=$$.tmpbam | |
| 12 # TMPBAM2=$$.tmpbam2 | |
| 13 # samtools view -bS $SAM > $TMPBAM | |
| 14 # samtools sort $TMPBAM $TMPBAM2 | |
| 15 | |
| 16 CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF" | |
| 17 | |
| 18 echo "CMD: "$CMD | |
| 19 eval $CMD | |
| 20 # rm $TMPBAM | |
| 21 # rm $TMPBAM2.bam |