How do I perform MAF analysis for each family separately in PLINK?
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7 months ago

I have a ped and a map file with 90 populations, and I wish to perform a MAF filter on each of those populations separately, using PLINK. The final output could be individual outputs for each family or in the best scenario, a dataset with the variants remaining (or excluded) from each of the families.

Should I first split the map and ped files in 90 other map and ped files (one for each family) and then execute the PLINK command for each of the populations? Or is there a way for PLINK to do both of these steps at once?

Thanks in advance!

plink family population split MAF • 251 views
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7 months ago
Sam ★ 3.8k

Haven't done this before, but if each of your population were properly coded as a family, then maybe you can use --freq --family

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It worked perfectly!! It created the table just like I wanted, now I just need to filter it based on the column "MAF". Thank you very much.

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Could you please move this comment to an answer, so I can close the post? I apologise, I'm new to this website and don't know exactly how to proceed.

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