ancestryinformativemarkers

Public AIMs

Most SNPs in genes are actually not that helpful for population stratification, being under selective pressure, so here are some ancestry informative snps that actually distinguish populations.

Also, you are not supposed to overload a PCA with SNPs that are already in LD.

These are in hg38

• UTAIM250 https://github.com/chenlabgccri/UT-AIM250 (also see https://github.com/radygenomics/AIM250-FOUR-CLADE/)
• Visage https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8391248/
• Seldin https://pubmed.ncbi.nlm.nih.gov/18683858/

Also see:

• Peddy https://raw.githubusercontent.com/brentp/peddy/master/peddy/GRCH38.sites