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 = "";
  my $annot = $fields[7];
  foreach my $alt (@alts) {
    next if (length($ref) > 50 || length($alt) > 50);
    if (length($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;