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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

FilterFuncotations Duplicate key error

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    Genevieve Brandt (she/her)

    Hi Azza, 

    We took a look at the stack trace and this looks to be a GATK bug in FilterFuncotations. There are two transcripts for the same gene (DDX11L1: ENST00000450305.2 and ENST00000456328.2) and the way that this code is written assumes that each gene only has one transcript. 

    I created a ticket for our development team to fix this bug here. However, since this is an experimental tool, it is not our highest priority to solve first. You can follow along with the ticket for when it will be solved. 

    Thank you for writing into the forum!

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Azza Ahmed the team was able to get to this quite quickly, the PR fix is here and will be merged after some reviews.

    If you want to test that it works ahead of time, you can download the GATK branch tb_fix_build_max_maf_rule and run FilterFuncotations from that version.

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    Azza Ahmed

    Great! Thank you very much.

    I will experiment with it and get back to you.

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    Genevieve Brandt (she/her)

    Thank you Azza Ahmed! It will definitely help with our testing.

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    Azza Ahmed

    Thank you again for the quick fix. I’m happy to confirm FilterFunctotator now resolves such transcript issues gracefully, and the pipeline runs to completion successfully- producing expected outputs.

    I note however that all the variants in my file (1 sample, WGS) are annotated as NOT_CLINSIG. I wonder why/how.

    Looking at the logs from the Functotator itself, I note the warnings and errors below- are they normal/benign?

    Again, much due gratitude for your help.

    Azza

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    Genevieve Brandt (she/her)

    These warnings are fine, they are just indicating at these sites with an alternate allele of a spanning deletion are not able to be annotated functionally: https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-

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    Genevieve Brandt (she/her)

    Azza Ahmed thank you for your help in testing the PR! The fix has been successfully merged and is in our newest release of GATK, 4.2.3.0: https://gatk.broadinstitute.org/hc/en-us/articles/4409678362139

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