How to calculate SNP frequency for each population in bfile using plink?
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3 months ago
Rudra • 0

Frequency • 235 views
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What have you tried?

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I have tried plink --bfile data --freq --out freq

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Always mention what you need, what you have tried, what you get from your trials and how this differs from what you need. Outlining the above will help you and others solve your problem quickly.

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above command give overall frequency, i want frequency for each population separately..

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How are you incorporating the sample to population mapping? Imagine an Excel spreadsheet with variants in each row and samples in each column. Where is the information that gives you the population identifier given the sample identifier?