Question: How to create population allele frequencies for common SNPS input file for iAdmix?
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gravatar for BusinessJim
5 months ago by
BusinessJim10
BusinessJim10 wrote:

I am trying to get to grips with iAdmix and I can run it using the data they provide but unfortunately I haven't been able to generate my own population allele frequencies to use as inputs.

On the GitHub page they say"

population allele frequencies for common SNPs (generated using HapMap3 genotypes or other genotype datasets)

I would like to use the whole HapMap3 data set but I have no idea how to do that, could anyone point me in the right direction?

next-gen genome • 237 views
ADD COMMENTlink written 5 months ago by BusinessJim10

For allele frequency, one can use dbSNP. Copy/pasted from https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/:

dbSNP RefSNP data now includes allele frequency data from 1000 Genomes and TOPMED populations.

ADD REPLYlink written 5 months ago by cpad01123.7k
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