vcfbiallelic

#!/usr/bin/env perl
# Remove anything that is not biallelic

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