Mercurial > repos > ulfschaefer > phe_samtools_mpileup
annotate phe_samtools_mpileup.sh @ 9:17996fd454c6 draft
Uploaded
author | ulfschaefer |
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date | Mon, 21 Dec 2015 09:00:43 -0500 |
parents | 65b5406977c9 |
children | f78ed0f61f52 |
rev | line source |
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3 | 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 |