Prevent SNPs being filtered out due to MAF in PLINK
During a recode step in plink, I do use the --MAF command to filter out some SNPs. However, I want to retain a specific SNP regardless of its MAF. How can I achieve that?
Thank you!
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chrchang523
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D H •
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D H •
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Assuming your variants have unique IDs, one option is: 1. Use --write-snplist to generate a list of SNPs passing your MAF filter. 2. Add your non-passing SNP to that list. 3. Use --extract on the augmented list.
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