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!
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!
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