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Genevieve Brandt

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Latest activity by Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Germline
    3. VariantRecalibrator incompatible contigs

    Another note - LiftoverVcf may be useful. https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard-

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    Genevieve Brandt commented,

    1. Community
    2. Germline
    3. VariantRecalibrator incompatible contigs

    Hi Mike Zhu, this is an issue with dbSNP using a different naming convention (1,2,... instead of chr1,chr2,...). We are looking for a solution with our tool Funcotator at this link here: https://gi...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Somatic
    3. Create Somatic PON threshold

    Hi Pedro Miguel Raposo: Please see this for more information about the Mutect2 algorithm: https://www.biorxiv.org/content/10.1101/861054v1 The GATK support team is focused on resolving questions ...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Germline
    3. Map reads to a reference with alternate contigs like GRCH38 using GATK4

    Hi neethukrishna Kausthubham, The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one,...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Germline
    3. gVCF reproducibility

    Hi Gaurav1983, please see this document for troubleshooting: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant If that ...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Somatic
    3. Germline Resouce

    Hi happyhihello, The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are build...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Non-Human
    3. java.lang.IllegalArgumentException: MALFORMED

    Has GATK worked for other commands for you? Also please run ValidateVariants to check if your VCF is in the correct format and post command and output. This also does not look like the entire stack...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Germline
    3. HaplotypeCallerSpark - error

    Hi stanedav, thank you for posting about this. This looks like a bug and we have created an issue ticket to solve the problem. You can follow along here: https://github.com/broadinstitute/gatk/issu...

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    • Genevieve Brandt
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    Genevieve Brandt commented,

    1. Community
    2. Non-Human
    3. VariantFiltration undefined variable

    Hi wbsimey, you mentioned that you did this same workflow before with an older version of GATK. What version was that? Was it with the same data?  I also noticed that you are using SelectVariants t...

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    Genevieve Brandt commented,

    1. Community
    2. Other
    3. Speeding up GATK4 DepthOfCoverage

    Hi Michael Franklin, I got more information about this tool in case you could get some runtime improvements. One question to consider, are you running this in a shared resources cluster with slow d...

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    • Genevieve Brandt
    • 1 vote