newbie: how to compare "sameness" of two samples using Illumina AB allele format data

Question

[scuffster]

Hi,

I have existing data on diploid samples, their SNPs, and Illumina AB format values for each SNP. Given a new sample, I want to determine how closely it matches the genotype of any of my existing samples. I'd really appreciate anyone's thought on how to approach this. Is it a case of repeating the pairwise comparison of the given sample by aligning SNPs and seeing if the allele values match? Are there any python or R modules that it would be best for me to use for this?

Many thanks for your help - Derek

Answer 1

[Kevin Blighe]

You could just aim to do an identity-by-state analysis.

Kevin