Question: newbie: how to compare "sameness" of two samples using Illumina AB allele format data
gravatar for scuffster
6 months ago by
scuffster0 wrote:


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

ADD COMMENTlink modified 6 months ago by Kevin Blighe65k • written 6 months ago by scuffster0
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

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


ADD COMMENTlink written 6 months ago by Kevin Blighe65k
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