Mercurial > repos > ulfschaefer > phephenix
comparison filter_vcf.sh @ 0:cb29f95c7b88 draft
Uploaded
author | ulfschaefer |
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date | Mon, 09 May 2016 09:27:06 -0400 |
parents | |
children | e2ee6acf8752 |
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-1:000000000000 | 0:cb29f95c7b88 |
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1 #!/bin/bash | |
2 | |
3 # echo $@ | |
4 | |
5 OUTPUT=$1 | |
6 shift | |
7 VCF=$1 | |
8 shift | |
9 ONLYGOOD=$1 | |
10 shift | |
11 FILTERS=$@ | |
12 | |
13 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') | |
14 | |
15 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" | |
16 | |
17 if [ $ONLYGOOD != "NOTTHERE" ]; then | |
18 CMD="$CMD --only-good" | |
19 fi | |
20 | |
21 echo "CMD: "$CMD | |
22 eval $CMD |