Prevent SNPs being filtered out due to MAF in PLINK

Question

[D H]

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!

Answer 1

[chrchang523]

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.