File: vcfremovenonATGC

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libvcflib 1.0.12%2Bdfsg-1
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#!/usr/bin/env perl
# Remove non-nucleotides in REF or ALT

while (<STDIN>) {
    if ($_ =~ /^#/) {
        print;
    } else {
        $_ =~ /^(.+?)\t(.+?)\t(.+?)\t(.+?)\t(.+?)\t/;
        $chrom = $1;
        $pos = $2;
        $tag = $3;
        $ref = $4;
        $alts = $5;
        $hasJunk = 0;
        @alts = split(/,/, $alts);

        if (!($ref =~ /A|T|G|C/)) {
            $hasJunk = 1;
        }
        foreach $alt (@alts) {
            if (!($alt =~ /A|T|G|C/)) {
                $hasJunk = 1;
            }
        }
        if (!$hasJunk) {
            print;
        }
    }
}