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

GATK funcotator transcript selection criteria



  • Official comment
    Genevieve Brandt (she/her)

    Hi Qing Zhang,

    Thanks for writing into the forum with this question!

    1. We have a description of how canonical is defined in our Funcotator information and tutorial article here. Please let me know if you have follow up questions after taking a look there.
    2. We don't have exact information on how the transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt list file is made. The list contains most relevant transcripts for somatic disease processes. Funcotator will preferentially annotate these transcripts. If there are none, it will fall back on canonical selection mode.

    Hope this helps!



    Comment actions Permalink
  • Avatar
    Pamela Bretscher

    Hi Qing Zhang,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.



    Comment actions Permalink
  • Avatar
    Bhavneet Bhinder

    Hi, I have a similar issue with EGFR variants. I used the --transcript-list option with ENST00000275493.7 (so I could get variant p.L858R), but the annotation still prioritizes transcript ENST00000455089.5 (p.L813R). How do I fix this issue please? 

    Comment actions Permalink
  • Avatar
    Jonn Smith

    Bhavneet Bhinder - The quickest thing I can suggest is to run Funcotator in `all transcripts` mode (`--transcript-selection-mode ALL`).  This will give you every transcript annotation for all of your variants and you can see if the one you want is there.  Is this an HG38 or HG19 variant?  Which version of the Funcotator data sources are you using?

    For a more in-depth look, can you please do the following:

    • open a new ticket on the GATK github
    • describe the issue
    • add your command-line invocation of GATK
    • include the variant you're investigating



    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk