--setFilteredGtToNocall

shanzorshanzor canberraMember

Hi,

I am trying to set filtered genotypes to no-call:

java -Xmx6g -jar GenomeAnalysisTK.jar
--analysis_type SelectVariants
--reference_sequence Egrandis_297_v2.0.fa
--variant filter_test.vcf
--setFilteredGtToNocall

following:

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

I'm getting this error MESSAGE: Argument with name 'setFilteredGtToNocall' isn't defined.

I can't find anything about this argument elsewhere in the gatk documentation or elsewhere online to point me int he right direction for its usage. Does it work?

Cheers
Shannon

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Make sure you're using the latest version as this argument was introduced very recently.

  • shanzorshanzor canberraMember

    Thanks I'll update and try again.

  • shanzorshanzor canberraMember

    Tried using 3.4.46. I think this is the latest version? Still getting the same Error.

    Actually there are two versions of this argument presented on the gatk web documentation at present.

    --setFilteredGtToNocall

    and

    --setFilteredGenotypesToNocall

    Not knowing if one was incorrect I tried both and same result.

    Any further suggestions?

    Cheers
    Shannon

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    That's odd, it should work in 3.4-46. Are you sure you're calling the right version of GATK, if you have eg an environment variable set up as shortcut to the GATK jar? It works for me when I test it locally with the latest official release.

    The two versions of the argument are due to a copy error that has been fixed internally, sorry about that. The doc will be refreshed when the next release happens (soon-ish).

  • shanzorshanzor canberraMember

    My bad, I hadn't reset the environment. Working now with --setFilteredGtToNocall. Thanks!

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