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?
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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