I was wondering if someone could help.
When using the 1000Genomes browser I came across this statement “1000 Genomes individual genotypes display” on the search results page , if I understand correctly this means that individual genotypes for any variant are not stored in the Ensemble database but instead in the 1K Genomes database (public mysql instance).
If that is true, we can view the genotypes from the 1K genomes browser, but which table in the database contains this information?
There is table named “compressed_genotype_single_bp”, is the table that contains this info. Also, if this the table then how does one convert the binary data fields back to text.
I am trying determine the genotype for several variants and working with the individual chromosome VCF files is not turning out to be practical, it’s very, very slow and has a huge computational overhead.
Any help in this direction will be highly appreciated.
When using the 1000Genomes browser I came across this statement “1000 Genomes individual genotypes display” on the search results page , if I understand correctly this means that individual genotypes for any variant are not stored in the Ensemble database but instead in the 1K Genomes database (public mysql instance).
If that is true, we can view the genotypes from the 1K genomes browser, but which table in the database contains this information?
There is table named “compressed_genotype_single_bp”, is the table that contains this info. Also, if this the table then how does one convert the binary data fields back to text.
I am trying determine the genotype for several variants and working with the individual chromosome VCF files is not turning out to be practical, it’s very, very slow and has a huge computational overhead.
Any help in this direction will be highly appreciated.