1000 genomes genotypes interpretation

Question

[cocchi.e89]

Dear all, I am working on some variants and comparing them with 1000 genomes data. I would like to retrive the number of homozigote patients for the variant, the 1000g VCF file looks like a long list of 0|0 (or 1/2). I looked at their website (http://www.internationalgenome.org/category/genotypes/) but it is still unclear to me, how would a ALT HOM be specified? And an ALT HEM? What is the difference between 0|1 and 0|2 for example.

Thanks a lot in advance for any help!

Answer 1

[Pierre Lindenbaum]

VCF specification https://samtools.github.io/hts-specs/VCFv4.2.pdf . section 1.4.2 "genotype fields"