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Variant Discovery in High-Throughput Sequencing Data

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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

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    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.

    Best,

    Pamela

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    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!

    Best,

    Genevieve

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