Filter by completeness with VCFtools

[AP38]

Hello,

What is the best way to filter for completeness with VCFtools?

Basically, I would like to only keep SNPs that are present in all individuals (or in 80% of all individuals). I have been using --max-missing or --max-missing-count but I am unsure if it is the right way of doing it.

Any thoughts would be greatly appreciated!

[SNPsaurus]

That is what those options are designed to do so I think you have a good solution.

[AP38]

Thanks, this is something that I wanted to double check - I have never filtered for completeness and wanted to make sure that I am using the appropriate flags.