File: vcfnoindels

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libvcflib 1.0.12%2Bdfsg-1
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#!/usr/bin/env perl
# Remove INDELs

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