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Matt Johnson

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Latest activity by Matt Johnson
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    Matt Johnson created a post,

    What happens with VariantRecalibrator when annotations are missing?

    1. Community
    2. Germline

    REQUIRED for all errors and issues: a) GATK version used: 4.2.6.1b) Exact command used: gatk VariantRecalibrator \-R GRCh38.fasta \-V Input.vcf.bgz \--resource:hapmap,known=false,training=true,trut...

    • Matt Johnson
    • 2 followers
    • 1 comment
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    Matt Johnson commented,

    1. Community
    2. Germline
    3. Joint Call WGS with a Large Cohort

    Laura Gauthier, thanks! This was immensely helpful, as we were trying to hold on to not subdividing intervals. Certainly gives us a better option that doesn't take multiple months.

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    Matt Johnson created a post,

    Joint Call WGS with a Large Cohort

    1. Community
    2. Germline

    I'm currently trying to joint call variants on a cohort ~4,000 human samples of WGS data. I've previously used the WGS calling interval list provided in the resource bundle, but even running on our...

    • Matt Johnson
    • Edited
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    Matt Johnson commented,

    1. Community
    2. General Discussion
    3. How do i manage jobs using cromwell on remote server cluster?

    I'm working on the same thing right now, though our server is in the process of being replaced right now and we're switching to a new cluster, so I'm in a bit of limbo. My plan is to pipe the submi...