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13
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1 #!/usr/bin/perl -w
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2
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3 use Getopt::Long;
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4
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5 #Initialize values
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6 my (@queries,@HEADER,$samples,@HEADER_OUT,$end,$samp);
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7 GetOptions ("query|q=s" => \$queries);
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8 if(!$queries){die "Usage: FORMAT_extract.pl <VCF> -query nSC
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9 \n\n";}
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10
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11
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12 open (VCF,"$ARGV[0]") or die "Usage: <VCF>";
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13
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14 while (<VCF>) {
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15 if($_=~/^##/){print;next}
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16 chomp;
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17 @line=split(/\t/,$_);
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18 if($line[0]=~/^#CH/){
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19 print join ("\t",@line,$queries)."\n";
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20 next}
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21 @FORMAT=split(/:/,$line[8]);
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22 @SAMPLE=split(/:/,$line[9]);
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23 for($i=0;$i<@FORMAT;$i++){
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24 if($FORMAT[$i] =~/^$queries$/){print join ("\t",@line,$SAMPLE[$i])."\n";next}
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25 }
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26 }
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27 close VCF;
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