Mercurial > repos > ulfschaefer > phephenix
annotate filter_vcf.sh @ 18:ec61f77332ff draft default tip
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| author | ulfschaefer |
|---|---|
| date | Tue, 10 May 2016 09:06:04 -0400 |
| parents | 4e64e338cc06 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/bash |
| 2 | |
| 16 | 3 # echo $@ |
| 0 | 4 |
| 5 OUTPUT=$1 | |
| 6 shift | |
| 7 VCF=$1 | |
| 8 shift | |
| 15 | 9 ONLYGOOD=$1 |
| 10 shift | |
| 0 | 11 FILTERS=$@ |
| 12 | |
| 13 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') | |
| 14 | |
| 15 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" | |
| 16 | |
| 15 | 17 if [ $ONLYGOOD != "NOTTHERE" ]; then |
| 18 CMD="$CMD --only-good" | |
| 19 fi | |
| 20 | |
| 0 | 21 echo "CMD: "$CMD |
| 22 eval $CMD |