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exclude uncalled variants using SelectVariants

blueskypyblueskypy Posts: 229Member

how to remove those variants with "./."?

Thanks a lot!

Answers

  • pdexheimerpdexheimer Posts: 463Member, GATK Dev, DSDE Dev mod

    Sample level selection is troublesome - do you exclude if any are uncalled? If all? Something in between?

    You could probably filter on AN to get what you're looking for - AN should be equal to 2 * (number of called samples), so you could pick a threshold and select that way. Also, there's an excludeNonVariant option that will remove variants that are ./. or 0/0 in all selected samples

  • blueskypyblueskypy Posts: 229Member
    edited November 2013

    hi, Pdexheimer, thanks so much for your help!
    Just to confirm, the "-env" option will also remove "./."?

    Post edited by blueskypy on
  • pdexheimerpdexheimer Posts: 463Member, GATK Dev, DSDE Dev mod

    Hmm, perhaps not. It looks like all the relevant tests in VariantContext only make sure that the called alleles are invariant, they completely ignore uncalled alleles. You may have to work directly with AN after all.

    Of course, I could be wrong - this is just my interpretation of the code. If you've got a test case, try it and see!

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