Mercurial > repos > ulfschaefer > filter_vcf

annotate filter_vcf.sh @ 4:5dfc843979c2 draft

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author ulfschaefer
date Fri, 11 Dec 2015 10:07:49 -0500
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1 #!/bin/bash
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3 OUTPUT=$1
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4 shift
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5 VCF=$1
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6 shift
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7 FILTERS=$@
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9 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
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10 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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11 export PATH=$PATH:$DIR
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12 CMD="filter_vcf.py --vcf $VCF --filters $FILTERS --output $OUTPUT"
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13
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14 echo "CMD: "$CMD
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15 eval $CMD