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Arosato

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Latest activity by Arosato
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    Arosato commented,

    1. Community
    2. Special GATK Use Cases
    3. GATK-SV GenotypeBatch: svtk count error

    Hi Genevieve, I figured as much, perhaps I can convince my group to investigate running the GATK-SV single sample terra workflow. Thanks for getting back to me! Best,  Andrew

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    Arosato created a post,

    GATK-SV GenotypeBatch: svtk count error

    1. Community
    2. Special GATK Use Cases

    Version Used Latest master branch as of [Feb 22 2022] https://github.com/broadinstitute/gatk-sv/ I am running the GATK-SV pipeline in Single sample mode (GATKSVPipelineSingleSample.wdl) with the ...

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    Arosato commented,

    1. Community
    2. General Discussion
    3. HaplotypeCaller Input Inquiry

    Hi Pamela,  That's exactly the information I was looking for! Thanks for your response and the article link! Best,  Andrew

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    Arosato commented,

    1. Community
    2. General Discussion
    3. HaplotypeCaller Input Inquiry

    Hi Pamela, Thanks for the response, unfortunately this answer leaves me with more questions. I am running the https://app.terra.bio/#workspaces/help-gatk/GATK4-Germline-Preprocessing-VariantCalling...

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    Arosato created a post,

    HaplotypeCaller Input Inquiry

    1. Community
    2. General Discussion

    Hi GATK Team,  I was looking at the Tool page for the  4.2.4.1 HaplotypeCaller found at https://gatk.broadinstitute.org/hc/en-us/articles/4414586765723?page=1#comment_4638698103451  I noticed the m...

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    Arosato commented,

    1. Tool Index
    2. 4.2.4.1
    3. HaplotypeCaller

    Hi GATK Team,  I noticed the message "Input bam file(s) from which to make variant calls" in the Input subsection. Further down, I noticed in the Haplotype Specific Arguments section that the --inp...