19 lines
436 B
Perl
Executable File
19 lines
436 B
Perl
Executable File
#!/util/bin/perl
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$|++;
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use strict;
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if (scalar(@ARGV) != 1 ) {
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die("usage vcf_to_germline_maflite.pl <normalAlias>\n");
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}
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my ($normalAlias) = @ARGV;
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my $line;
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while (defined($line = <STDIN>)) {
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if ($line =~ /#/) { next; }
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my ($chrom, $pos, $rsName, $ref, $alt) = split("\t", $line);
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my $ncbiBuild = "36";
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print join("\t", ($ncbiBuild, $chrom, $pos, $pos, $ref, $alt, $alt, $normalAlias, $normalAlias)) . "\n";
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}
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