detecting SNP allele and genotype frequencies from 1000 genomes at ensembl

Question

[Viktor Bojovic]

For each variation name (e.g. rs2242480) i would like to get data for table like this which was taken from here

Here is one sample that i have to get for one subpopulation:

Population: ACB;1000GENOMES:phase_3:ACB

Allele: frequency (count) C: 0.208 (40) T: 0.792 (152)

Genotype: frequency (count) C|C: 0.418 (1047) C|T: 0.320 (802) T|T: 0.262 (655)

I have connected to homo_sapiens_variation_84_38 database at ensembl mysql server. Then I have been searching through alleles joining with variations and populations, but i cannot find any of those populations enlisted in table. I have also used population_structure table, but it didnt help. So i wanted to ask if anyone can help me with info how to extract this data. Thanx in advance

Answer 1

[Denise CS]

The genotype and allele frequency data from the 1000 Genomes project is far too large to be stored efficiently in the Ensembl MySQL schema. You would need to get that information via the Variation API, which uses a custom VCF backend to retrieve the data and return it on the web interface (as you linked out to). So you can only access this data via the Ensembl API or through the VCF files directly. More details can be found in Will McLaren's post

Answer 2

[Viktor Bojovic]

thank you very much