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  • AP38
    Member
    • May 2016
    • 14
    #1

    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!
    Tags: completeness, filter, vcftools
  • SNPsaurus
    Registered Vendor
    • May 2013
    • 525
    #2
    That is what those options are designed to do so I think you have a good solution.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment

    • AP38
      Member
      • May 2016
      • 14
      #3
      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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