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Samantha Zarate

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Latest activity by Samantha Zarate
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    Samantha Zarate commented,

    1. Community
    2. General Discussion
    3. VariantEval IndexOutOfBoundsException

    Hi Genevieve-Brandt-she-her, let me clarify what I mean. I'm comparing VCFs generated using two reference genomes, GRCh38 and CHM13. CHM13, as an organism, doesn't have a Y chromosome, so it's been...

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    Samantha Zarate commented,

    1. Community
    2. General Discussion
    3. VariantEval IndexOutOfBoundsException

    Hi Genevieve-Brandt-she-her, thanks for the insight! How would you recommend combining X and Y population-scale VCF files, given that the samples are not the same between the two (not every sample ...

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    Samantha Zarate created a post,

    VariantEval IndexOutOfBoundsException

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    1. Community
    2. General Discussion

    a) GATK version used: v4.1.9b) Exact command used: /gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar \ VariantEval \ -R /$PATH_TO_REFERENCE/chm13/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270...

    • Samantha Zarate
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    Samantha Zarate commented,

    1. Community
    2. Germline
    3. Using GenotypeGVCFs with GenomicsDB

    Update: I resolved this error by replacing `gendb:///gs://` with `gendb.gs://`. If this could be added to the documentation, that would be very helpful!

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    Samantha Zarate created a post,

    Using GenotypeGVCFs with GenomicsDB

    1. Community
    2. Germline

    Hello, I am using Terra to run GenotypeGVCFs on a GenomicsDB that exists in Google Cloud and therefore is a `gs://` URI. I generated it by using `GenomicsDBImport` with the output specified as `gs:...

    • Samantha Zarate
    • Edited
    • 2 followers
    • 2 comments
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