I need a way to get the genotype frequencies for different populations for various SNPs (so I need to be able to supply an RSID, then get a list of its genotype frequencies). I installed the Ensembl Perl API and found the tutorial on the variation module: http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag

The problem is, in the tutorial it tells you how to get allele frequencies for SNPs, but doesn't mention any way to get genotype frequencies. For alleles, you can do this:

my $variation = $variation_adaptor->fetch_by_name('rs1333049');

my $alleles = $variation->get_all_Alleles();

foreach my $allele (@{$alleles}) {
  next unless (defined $allele->population);
  my $allele_string   = $allele->allele;
  my $frequency       = $allele->frequency || 'NA';
  my $population_name = $allele->population->name;
  printf("Allele %s has frequency: %s in population %s.\n", $allele_string, $frequency, $population_name);
}

but for info on genotypes, they only have this method:

my $variation = $variation_adaptor->fetch_by_name('rs1333049');

# OPTIONAL: uncomment this line to retrieve 1000 genomes phase 3 data also
# $variation_adaptor->db->use_vcf(1);

my $genotypes = $variation->get_all_SampleGenotypes();

foreach my $genotype (@{$genotypes}) {
  print "Sample ", $genotype->sample->name, " has genotype ", $genotype->genotype_string, "\n";
}

I was thinking maybe I could calculate the genotype frequency from the allele frequencies, but to do that I'd need to know the allele count wouldn't I? I don't know if the API lets you get allele counts. All that is what they show on the tutorial, maybe there are more features in there that they don't mention in the tutorial?