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Funcotator datasources.v1.7 gencode raise error



  • Official comment
    Jonn Smith

    Tjitske - I responded to your github post, but in case you didn't see it:


    @Tjitskedv Typically we ask people make a new issue in github or create a forum post, rather than commenting on open pull requests.

    To answer your question directly - do not use v1.7 datasources with GATK 4.1.7.X or 4.1.8.X. Those data sources are not yet compatible with the Funcotator code in the Master branch. When we release GATK they will work with Funcotator. This is not a bug in the code - it is an artifact of how we have to do data source releases.

    See issue #6708 for all the gory details.

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    Genevieve Brandt (she/her)

    Hi Tjitske de Vries, it looks like there is an issue with compatibility between your files. Where did you get your GTF file? Also, are any of your data sources using hg38 instead of hg19? This will lead to errors.

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    Tjitske de Vries

    Hi Genevieve Brandt, thank you for your response. I downloaded the GTF file as part of the bundle  funcotator_dataSources.v1.7.20200521s.tar.gz from

    al my datasources are hg19, I did not make any new data sources, only use those of the provided bundle.

    I have used a Mutect2 vcf file which was filtered by FilterMutectCalls, I use the exact same reference file for all steps. 

    Is there something that I can test/check/change for the compatibility? (removing gencode datasource is not an option since this is the only one that is required.) - do I need another version? 

    Hope you can help

    Update: I have downloaded the v1.6 data source bundle which contained the genecode V19 file now I used that gencode file instead of the one from v1.7, (copied it to the v1.7 folder so did not change any other file) and now it works. So I think the genecode-backmap file is not really compatible with funcotator for hg19, was this tested? or is this problem specific for my files? it seems to be a more general problem, so maybe good to check and update the files of the data source bundle?

    kind regards Tjitske

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