convert_vcf_2_bed

#!/usr/bin/perl

use warnings;
use strict;
use POSIX qw(ceil floor);
use File::Basename;
use File::Path;
use Getopt::Long;
use Pod::Usage;

=head1 NAME

convert_vcf_2_bed

=head1 SYNOPSIS

convert_vcf_2_bed [options] <filename>

    -v  verbose
    -d  debug
    -o  output contig directory.

    usage: convert_vcf_2_bed input.vcf

    Converts a VCF file into a corresponding bed file.

=head1 DESCRIPTION

=cut

#option variables
my $help;
my $outputBEDFile;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions ('h'=>\$help,
                'o:s'=>\$outputBEDFile)
    || scalar(@ARGV)!=1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

if ($outputBEDFile =~ /bed.gz$/)
{
    open(OUT, "| bgzip -c > $outputBEDFile");
}
else
{
    open(OUT, ">$outputBEDFile");
}

my $inputVCFFile = $ARGV[0];
open(IN, "vt view $inputVCFFile |") || die "Cannot open $inputVCFFile";

while (<IN>)
{
    chomp;

    my ($chrom, $pos, $id, $ref, $alt, $others) = split("\t");
    
    --$pos;
    
    print OUT "$chrom\t$pos\t" . (length($ref)+$pos) . "\n";
}

close(IN);
close(OUT);