What tool should I use to identify the ancestry (e.g EUR or TSI or CEU) of a single human using genotyped VCF file?

Question

[shajib.sust]

Hi,

I have genotyped a single person from Platinum Genome dataset of Illumina. I want to identify the ancestry of this person (NAXXXXXX) using his/her genotyped VCF file and population panel data (e.g. EUR or TSI or CEU) from hapmap. What tool should I use to do that? Any literature explaining the method to do it will also be very helpful for me. Please suggest...

With Kind Regards,

-Ruhul

Answer 1

[Philipp Bayer]

I'd download the HapMap data from PLINK, merge that with your vcf data using PLINK2 --merge, then run any population stratification program on that and see where your single data point clusters -

I can recommend fastSTRUCTURE since that one uses PLINK's bed as input, or EIGENSTRAT which gives you a nice PCA plot but is a bit harder to run.

Alternatively, you could just get a list of ancestry-related SNPs ("Ancestry Informative Markers", like here: http://www.nature.com/ejhg/journal/v22/n10/full/ejhg20141a.html ) and manually compare your SNPs, that's easier but a bit more messy.