The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

exclude uncalled variants using SelectVariants

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

Thanks a lot!



  • 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 Member
    edited November 2013

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

  • 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!

Sign In or Register to comment.