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user438383
user438383
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Chosing an imputation pannelpanel for SNP-Chip data?

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Dan Bolser
Dan Bolser
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Chosing an imputation pannel for SNP-Chip data?

I have about 1,000 SNP-Chip data (samples) that I'd like to impute over (for the purpose of having more rsIDs to match against GWAS data).

However, I don't know the ancestry of each sample / the ancestry hasn't been recorded in a reliable way.

Is there a 'quick and dirty' method to decide which imputation panel to use based on the genotype data itself? e.g.

  • sample 1 'looks' British in England and Scotland (GBR),
  • sample 2 'looks' Colombian in Medellin, Colombia (CLM),
  • sample 3 'looks' Bengali in Bangladesh (BEB), etc.

Once I know which group each sample matches most closely I can then perform imputation with the appropriate imputation panel.