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1 #!/bin/bash
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2
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3 output=$1;shift
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4 refg=$2
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5 input=${9}
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6
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7 command -v table_annovar.pl >/dev/null 2>&1 || {
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8 echo "ERROR : table_annovar.pl not found. Add annovar scripts to your galaxy path !" ;
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9 return 1 ;
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10 }
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11
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12 mkdir out
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13 name=${input##*/}
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14 name=${name%%.*}
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15
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16 perl $SCRIPT_PATH/mutspecAnnot.pl \
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17 --outfile out \
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18 --pathAVDBList $SCRIPT_PATH \
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19 --temp "./temp" \
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20 $* 2>&1
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21
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22 ls out/Mutational_Analysis/Annovar/
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23 cp out/Mutational_Analysis/Annovar/${name}.${refg}_multianno.txt $output
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24
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25 exit 0
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26
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