How to calculate SNP frequency for each population in bfile using plink?

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2.9 years ago

Rudra • 0

I want to calculate frequency of a SNP for each population in bfile using plink...Please help..!!Thanks in advance

Frequency • 852 views

ADD COMMENT • link updated 2.9 years ago by Ram 43k • written 2.9 years ago by Rudra • 0

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What have you tried?

ADD REPLY • link 2.9 years ago by Ram 43k

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

ADD REPLY • link updated 2.9 years ago by Ram 43k • written 2.9 years ago by Rudra • 0

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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.

ADD REPLY • link 2.9 years ago by Ram 43k

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

ADD REPLY • link 2.9 years ago by Rudra • 0

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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?

ADD REPLY • link 2.9 years ago by Ram 43k

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