Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mutect2 Funcotator interval error

Answered
0

3 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi Elise Valkanas (she/her),

    Thanks for writing into the forum with this issue, I can help you out to figure out what is going on here.

    I found a previous forum post where a user was having the same issue. It looks like the problem was determined to be a bug in 4.1.7.0, however, the github ticket has not been solved yet: https://github.com/broadinstitute/gatk/issues/6598.

    I can look into the problem further to try to determine a workaround. Could you verify that this issue persists in the latest version of GATK (4.2.3.0) with the new data sources? Please also provide your Funcotator command line and complete Funcotator program log.

    Best,

    Genevieve

    0
    Comment actions Permalink
  • Avatar
    Elise Valkanas (she/her)

    Hi Genevieve, 

    Thanks! Since this is a featured workspace I didn't think that the version of GATK would need to be updated, but looks like doing that and changing the Funcotator files did the trick. Thanks for the help!

    Elise

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Thanks for the update Elise and glad your problem is resolved!

    GATK 4.1.7.0 is a stable release so we still are using it for featured workspaces. I'll forward this information to my colleagues who work on those featured workspaces so that they can prioritize getting a new version of GATK tested.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk