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comparison filter_vcf.sh @ 0:cb29f95c7b88 draft

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author ulfschaefer
date Mon, 09 May 2016 09:27:06 -0400
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children e2ee6acf8752
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-1:000000000000 0:cb29f95c7b88
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