How to identify ethnicity of segment of single chromosome?

[Boudin]

I have a segment of 2,000 SNPs that 23andMe says is Finnish.

I think it's really Indigenous American mistaken for Saami.

I tried uploading a 23andMe file containing JUST that segment, but GEDmatch says the file isn't big enough. I was hoping to see if the matches were mostly Indigenous American or Finnish.

Any idea how I can figure out the truth?

Is it Finnish or Indigenous American or something else?

[calxpal]

The only idea I have is maybe getting Pro Admixture Studio from DNAGenics since it allows you to run various calculators (extremely similar to Gedmatch) and it allows you to select any segment you want by position (as long as there are enough SNP's). I've used this program myself for looking at certain segments and I think the accuracy is decent, although I think the accuracy varies by calculator.

I hope this suggestion might help or offer clues.

[Boudin]

The solution, I've recently learned, is to modify only the chromosome containing the segment of interest in the 23andMe file. Delete all rows for that chromosome except those containing the segment, then make each row homozygous for the segment's chromosome. So if the segment is on copy 2, and the genotype is AC, make the genotype CC instead.

Then upload the file to GEDmatch for research purposes, and you can immediately run K36 on each chromosome. Of course you are only interested in the results for the chromosome containing the segment of interest.

[Solitude]

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