Mercurial > repos > ulfschaefer > phe_phenix

annotate filter_vcf.sh @ 0:99ff94f3d11f draft

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author ulfschaefer
date Tue, 19 Apr 2016 11:59:39 -0400
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1 #!/bin/bash
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2
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3 echo $@
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4
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5 OUTPUT=$1
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6 shift
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7 VCF=$1
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8 shift
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9 FILTERS=$@
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10
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11 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
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12
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13 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"
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14
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15 echo "CMD: "$CMD
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16 eval $CMD