Is it possible to infer whether a patient is with homozygous with the alternative alleles (at two different location)

Question

[cwwong13]

I am using UK biobank SNP array data. I know that each of the SNP is represented in a row. However, I would like to get insight from gene-level results: that is whether an individual who has both alleles are in the form of an alternative allele (the one with less AF).

I know it is relatively easy to know if an individual is homozygous to a particular SNP, my question is to see if that is also possible to know if, for instance, an individual is heterozygous in SNP 1 and heterozygous in SNP 2, and these SNPs are located in different chromatin.

Answer 1

[d-cameron]

If you're using VCFs then this genotyping information should be available in the sample-level GT field (See section 1.6.2 of the VCF specifications https://samtools.github.io/hts-specs/VCFv4.3.pdf).

I know it is relatively easy to know if an individual is homozygous to a particular SNP

You just repeat what you did for a single SNP a second time. Each SNP will be in a separate VCF row, so you just need to look up two different rows instead of just the one.