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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

Issue when running BaseRecalibrator

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    Anthony Dias-Ciarla

    Hi Duo Xie,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.

    After consulting with our developers, it appears that the issue that you are encountering may be a bug. I’ve created a GitHub ticket where you can follow along with the progress as we try to fix this issue. Please find the link here.

    We appreciate you bringing this issue to our attention! Please let us know if you have any other questions in the meantime.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Duo Xie,

    I wanted to follow up with you on your inquiry with some updates. 

    The GATK developer that is best able to help solve your GitHub ticket is currently out of the office. They aren't due to be back until early next week. I wanted to keep you updated and let you know that we haven't forgotten about you.

    We truly appreciate your patience! If you have any additional questions/comments in the meantime, please do not hesitate to reach out anytime.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Duo Xie,

    Thank you for your much-appreciated patience! Our developer has returned from vacation and has responded to the GitHub thread. I wanted to write to you to let you know, just in case you didn’t see it.

    The developers think the issue may be related to the non-ASCII character in the temp file path.

    Łuksza_2022_Nature

    They would like you to try using a temp folder and output folders that contain only English characters. Java seems to have a recurrent problem with any non-ASCII characters.

    I hope this helps! Please let me know whether this fix leads you to success. If not, please reach back out; we will happily look further into what else might be causing this issue. Thank you again for your incredible patience.

    Stay well,
    Anthony

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    Duo Xie

    Hi Anthony Dias-Ciarla,

    Thank you for your work!

    I have given it a try and responded in the GitHub page: https://github.com/broadinstitute/gatk/issues/8005#issuecomment-1254561081

     

    Best,

    Duo

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    Anthony Dias-Ciarla

    Hi Duo Xie,

    I'm going to go ahead and solve this ticket. You should be able to continue following along with your GitHub ticket.

    Thank you again for your contribution to the GATK forum. If you need anything else from me, please do not hesitate to reach out!

    Best,
    Anthony

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