Mercurial > repos > ulfschaefer > filter_vcf

annotate filter_vcf.sh @ 0:834a312c0114 draft

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author ulfschaefer
date Thu, 10 Dec 2015 09:22:39 -0500
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1 #!/bin/bash
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2
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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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8
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9 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
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10
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11 CMD="filter_vcf.py --vcf $VCF --filters $FILTERS --output $OUTPUT"
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12
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13 echo "CMD: "$CMD
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14 eval $CMD