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Layne Sadler

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Latest activity by Layne Sadler
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    Layne Sadler created a post,

    Do GATK tools support Apple silicon?

    1. Community
    2. General Discussion

    I need to purchase a new laptop. I want to upgrade to a many-cored Mac with the new Apple silicon chips for parallelism, speed, and reduced power consumption. This is especially attractive for vari...

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    Layne Sadler commented,

    1. Tool Index
    2. 4.1.4.1
    3. HaplotypeCaller

    Does HaplotypeCaller support Apple silicon?https://www.biostars.org/p/478429/#495387

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    Layne Sadler commented,

    1. Tool Index
    2. 4.2.6.1
    3. Funcotator

    Here is a table comparing Funcotator to VEP variant classifications. It's not completely 1-1 as some of the high/moderate are missing. https://docs.google.com/document/d/1Xplvq-6wNUKQWUN7hsNPu_TFdy...

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    Layne Sadler commented,

    1. Community
    2. Documentation Questions
    3. Where is the list of annotations and annotation groups?

    Agreed that the annotations should have their own page to be more searchable

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    Layne Sadler commented,

    1. Tool Index
    2. 4.1.7.0
    3. HaplotypeCaller

    So I got this running (hope it finishes) after a few hours of troubleshooting. It would be nice to have links to information about upstream steps like generating the supplemental files like the fas...

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    Layne Sadler commented,

    1. Technical Documentation
    2. Glossary
    3. FASTA - Reference genome format

    The page in this error message does not exist """A USER ERROR has occurred: Fasta index file ... Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-us...

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    Layne Sadler commented,

    1. Tool Index
    2. 4.1.7.0
    3. HaplotypeCaller

    Error while following the annotation example verbatim:`A USER ERROR has occurred: Unrecognized annotation group name: Standard`

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    Layne Sadler commented,

    1. Getting Started
    2. Best Practices Workflows
    3. Germline short variant discovery (SNPs + Indels)

    Reference for HaplotypeCaller commands:https://gatk.broadinstitute.org/hc/en-us/articles/360042913231-HaplotypeCaller Prior that, the GATK subtools are found via `gatk -h` SortSam (Picard) = Sorts...

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