Mercurial > repos > ulfschaefer > phephenix
annotate filter_vcf.sh @ 5:e2ee6acf8752 draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Thu, 16 Jun 2016 06:39:37 -0400 |
| parents | cb29f95c7b88 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/bash |
| 2 | |
| 3 # echo $@ | |
| 4 | |
| 5 OUTPUT=$1 | |
| 6 shift | |
| 7 VCF=$1 | |
| 8 shift | |
| 5 | 9 REF=$1 |
| 10 shift | |
| 0 | 11 ONLYGOOD=$1 |
| 12 shift | |
| 13 FILTERS=$@ | |
| 14 | |
| 15 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') | |
| 16 | |
| 5 | 17 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT --reference $REF" |
| 0 | 18 |
| 19 if [ $ONLYGOOD != "NOTTHERE" ]; then | |
| 20 CMD="$CMD --only-good" | |
| 21 fi | |
| 22 | |
| 23 echo "CMD: "$CMD | |
| 24 eval $CMD |