Converts a vcf file (typically of indels) into a bed file

vcf2bed.pl

#!/usr/bin/perl

use strict;

if (scalar @ARGV != 1) {
	print "vcf2bed.pl <vcf_file>\n";
	exit 1;
}

my $vcfFile = $ARGV[0];

open VCF, $vcfFile
	or die "Cannot open $vcfFile";
	
while (<VCF>) {
	
	if (index($_, '#') == 0) {
		next;
	}
	
	my @fields = split /\t/, $_;
	
	my $chrom = $fields[0];
	my $startPos = $fields[1];
	my $ref = $fields[3];
	my @alts = split (/,/, $fields[4]);
	
	my $endPos = $startPos;
	my $indelCall = "";
	
	foreach my $alt (@alts) {
		
		if (length($ref) > length($alt)) {
			# deletion event
			my $diff = substr($ref, length($alt));
		
			$endPos = $startPos + length($diff);
			$indelCall = '-' . $diff;
		}
		elsif (length($alt) > length($ref)) {
			# insertion event
			my $diff = substr($alt, length($ref));
		
			$indelCall = '+' . $diff;
		}
		
		# print out the line
		print "$chrom\t$startPos\t$endPos\t$indelCall\n";
	}
	
	
}	

close VCF;