Extract genotypes from multisample VCF file using vcftools

extract-genotypes.pl

use strict;
use warnings;
use Vcf;

my $filename = $ARGV[0];

open ( my $handle, "<", $filename);
my $vcf = Vcf->new(fh=>$handle);
    $vcf->parse_header();
vcf_iterate();

sub vcf_iterate
{
  while ( my $x=$vcf->next_data_hash() )
  {
   foreach my $sample ( keys $$x{gtypes} )
   {
     print "SAMPLE=$sample, genotype_raw=$$x{gtypes}{$sample}{GT}, ";
     my $decoded_genotype = decode_genotype($x, $sample);
     print "decoded_genotype=$decoded_genotype\n";
   }
  }
}

sub decode_genotype
{
  my ( $x, $sample ) = ( $_[0], $_[1] );
  my $gt = $vcf->decode_genotype($$x{REF}, $$x{ALT}, $$x{gtypes}{$sample}{GT}); # returns 'G/G'
  return $gt;
}