Question

how would I find SNPs that are highly polymorphic between populations in dbSNP

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6.7 years ago

b10hazard ▴ 30

Hi there,

I’m trying to get a vcd file containing SNPs that are highly polymorphic by population. Does anything like this exist in dbSNP? I’m guessing I would want to find SNPs with high fixation indexes between populations but I have no idea how to do this. Any advice would be great. Thanks!

dbsnp SNP allele ncbi • 1.3k views

ADD COMMENT • link updated 6.7 years ago by agata88 ▴ 870 • written 6.7 years ago by b10hazard ▴ 30

score 0 · Answer 1 · 2018-03-14

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6.7 years ago

agata88 ▴ 870

This may help: How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Sliding Window?

You can download dbSNP database in vcf file and try vcftools to select those SNP of your interest.

Best, Agata

ADD COMMENT • link 6.7 years ago by agata88 ▴ 870