Removing SNPs with over 2% missing rate in plink

Question

[amitgourav.ghosh12]

I have a merged binary dataset and I want to remove SNPs with more than 2% missing rate in plink. How should I proceed? Thank you!

Answer 1

[Wietje]

Check out the PLINK manual (https://www.cog-genomics.org/plink/1.9/filter) and the --geno option, which allows you to filter for variants with a defined missing/ call rate.

Missing genotype rates

--geno {maximum per-variant} --mind {maximum per-sample}

--oblig-missing [variant x block file] [block definition file]

--geno filters out all variants with missing call rates exceeding the provided value (default 0.1) to be removed, while --mind does the same for samples.

[amitgourav.ghosh12]

Thank you very much for your help! I shall try out.