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Old 07-05-2016, 12:57 PM   #1
AP38
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Default Filter by completeness with VCFtools

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!
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Old 07-05-2016, 11:15 PM   #2
SNPsaurus
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That is what those options are designed to do so I think you have a good solution.
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Old 07-06-2016, 06:12 AM   #3
AP38
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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.
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