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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

Funcotator Custom Annotation Table Not Working

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4 comments

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    Anthony Dias-Ciarla

    Hi Etienne Mahe,

    Thank you for writing to the GATK Forum! We hope that we can help you solve this problem.

    Here are some initial suggestions:

    1. Confirm that the pathway in the error message is valid.
    2. Check for any spelling errors in the name of the file.
    3. Check that you can independently access the file.
    4. If the file does exist, ensure that you’ve permitted us to access it.

    Sometimes these errors are a simple fix; please try the above and let me know if it works. If not, please feel free to reach back out so we can take a deeper dive.

    Best,

    Anthony

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    Etienne Mahe

    Thanks Anthony,

     

    I can confirm your suggestions have been run through and do not solve the problem.

     

    I have identified a less-than-ideal work-around, however. GATK will accept a bed file for indexing. As such, I created an artificial bed file with the reference data that I want GATK to incorporate through Funcotator, with the first line including the fake elements "chr1\t0\t1\t" followed by the headers of the relevant data columns. This does work, as the bed file can be indexed and Funcotator will not complain about a lack of a idx file.

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    Anthony Dias-Ciarla

    Hi Etienne Mahe,

    Thanks for trying out those suggestions and providing this feedback! I’m glad you found a workaround, though I would like to fully identify the issue to ensure more ideal workflows in future versions.

    Could you please upload a zip/tar file of the folder of data sources that you attempted to create? The development team would like to take a closer look.

    For more detailed information on uploading a bug report to our FTP server, click here. Please let me know when you have successfully uploaded the data.

    Thank you!
    Anthony

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    Anthony Dias-Ciarla

    Hi Etienne Mahe,

    Please see my updated comment above. It looks as though I gave you some inaccurate information.

    Best,

    Anthony

     

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