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Layne Sadler

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Latest activity by Layne Sadler
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    Layne Sadler commented,

    1. Community
    2. Germline
    3. why I have a 1/1 genotype on chromosome X for males

    GATK should issue a warning when allosomes are detected without using appropriate ploidy options

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    Layne Sadler commented,

    1. Community
    2. Germline
    3. Calling variants on chromosome Y

    This is what I see for the chrX genotypes of a randomly selected male GT:count1/1:17020/1:3711/2:14 Consider that GQ>=15 means 95% confidence --- chrY is worse because the majority are labeled het...

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    Layne Sadler commented,

    1. Community
    2. Somatic
    3. SNP analysis returning way too many variants

    Make sure that vcf tools is actually applying your filters.  In high depth samples, lots of low quality variants creep in: https://www.biostars.org/p/9564606/

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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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