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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

Haplotypecaller 4.5.2.0 --alleles unexpected output

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    Genevieve Brandt (she/her)

    Hi Geert Vandeweyer,

    Thank you for writing in about this. We are not sure why these variants would be output and we would like to take a closer look. And just to double check - you are certain that these variants are not in your affected_alleles.vcf?

    Best,

    Genevieve

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    Geert Vandeweyer

    Yes, but I'll double check. If you can send me a private message, I can share the data. (Patient material)

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    Genevieve Brandt (she/her)

    Geert Vandeweyer okay thank you. You only need to provide a small portion of your BAM file, just around 100 bases before and after this region. We have instructions here for how to upload a bug report: https://gatk.broadinstitute.org/hc/en-us/articles/360035889671

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    Geert Vandeweyer

    Genevieve-Brandt-she-her : I've uploaded the data to the FPT client. Name == HaplotypeCaller.unknown_alleles.tar.gz

    There's one of the unexpected alleles called in the provided region. 

    Thanks for looking into it ! 

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    Genevieve Brandt (she/her)

    Hi Geert Vandeweyer,

    We took a look at your files, thank you for making the process so easy for us! 

    The only variant we were able to replicate on our end that was called in addition to chr5:125894866 was chr5:125895106. It does look like a bug and we think we have identified the cause as an edge case in the genotyper code. I have created a ticket in our repo so that our developer team can fix this issue: https://github.com/broadinstitute/gatk/issues/7741

    For your specific issue with these variants popping up now, you can always remove them with SelectVariants.

    Thank you for bringing this to our attention and please let me know if you have any other questions.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    We were able to get a fix for this that will be in the next GATK release. https://github.com/broadinstitute/gatk/pull/7740

    Thank you so much again for your very thorough files, they really helped us solve this quickly!

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    Geert Vandeweyer

    Thank you for looking into the problem ! 

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