Hi all,
I have a quite large set of SNPs from several geographically distinct populations. I want to estimate average allele frequencies for each SNP among, lets say, two-three westernmost and two-three eastern most populations.
As I understand, it is a rather trivial task for a plenty of further pipelines, but have no idea how to do it correctly.
Can I do it manually by calculating the arithmetic mean of AF value of each allele in each population (taken from vcf), and then calculating the arithmetic mean among particular populations, or maybe, this task should be solved by means of some utility using more complex mathematics?
Hi Danila
you can dig in the dbSNP tool from NCBI (https://www.ncbi.nlm.nih.gov/snp/rs28360521) and pick some data (the link shows you an example of one snp).
all the best
fred
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