File: vcfmultiallelic

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libvcflib 1.0.12%2Bdfsg-1
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#!/usr/bin/env perl
# remove anything that is not multiallelic

while (<STDIN>) {
    if ($_ =~ /^#/) {
        print;
    } else {
        $_ =~ /^(.+?)\t(.+?)\t(.+?)\t(.+?)\t(.+?)\t/;
        $chrom = $1;
        $pos = $2;
        $tag = $3;
        $ref = $4;
        $alt = $5;
        if ($alt =~ /,/) {
            print;
        } else {
            # remove anything which isn't multiallelic
        }
    }
}