Getting frequencies for multiple SNPs from dbSNP at once?
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9 months ago
devenvyas ▴ 680

I have about a thousand potential rare/private mutations from aDNA samples (representing a single archaeological population). These are sites that do not show up at all in 1000G phase 3 VCFs or a couple other datasets and do pass the 1000G GRch37 accessibility mask.

I want to get their allele frequencies en masse from dbSNP. Some of these could be a product of contamination, some could be real

Currently, the only way I know to get their frequencies is to put their coordinates into dbSNP one-by-one. Is there a way to do this with all of them at once. I have GRch37 coordinates for all of them and GRch38 coordinates from liftover for almost all of them.

dbSNP SNP • 388 views

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