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Stephanie Hoyt

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Latest activity by Stephanie Hoyt
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    Stephanie Hoyt commented,

    1. Tool Index
    2. 4.2.6.1
    3. PathSeqPipelineSpark

    Hello, The link to the resource bundle is broken. Where can I get the prebuilt references for a standard microbial set? Thanks.

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    Stephanie Hoyt commented,

    1. Community
    2. General Discussion
    3. using publicly available panel of normals

    Hello, Is there a publicly available 1000 genome HDF5 PON anywhere? We do not have enough samples to generate a PON ourselves with CreateReadCountPanelOfNormals.  Thank you, Stephanie

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    Stephanie Hoyt created a post,

    Cromwell: can't find file ID

    1. Community
    2. Somatic

    I am using Cromwell to test a CWL implementation of the GATK somatic CNV pipeline. I am currently getting the following error (full log at the end):   `` Cannot find a tool or workflow with ID file...

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    Stephanie Hoyt commented,

    1. Technical Documentation
    2. Glossary
    3. Panel of Normals (PON)

    Hi, The listed PON's are vcf format, but the GATK copy number pipelines require an hdf5 file. Is there another processing step we need to do before we can use these files?   Thanks.

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