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Derek Caetano-Anolles

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Latest activity by Derek Caetano-Anolles
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    Derek Caetano-Anolles commented,

    Hi Eva (Evander) -- Good question.  The variant calls were not made in the alt contig region, but were based on the Illumina masked reference available in the following DRAGEN-reference in the GCP ...

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    Derek Caetano-Anolles created an article,

    Masked reference genomes

    The work presented here includes significant contributions from Pankaj Vats and Harry Clifford from NVIDIA. —————————— Factors that affect genomic analysis When it comes to sequencing experiments, ...

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    Derek Caetano-Anolles commented,

    Eddy W - By default the VCF files will not recognize those variant sites as missing genotype. This would require converting the GenotypeGVCFs output to a format that PLINK will recognize, by replac...

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    Derek Caetano-Anolles commented,

    Thank you for your input, SAMUEL ANDREW ~ As you know, you can still determine the missing genotypes because the FORMAT DP will be 0 even within the current GenotypeGVCFs format. So it is still pos...

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    Derek Caetano-Anolles commented,

    Felipe Batalini Good catch. The video link has been updated. Thanks for bringing it to my attention!

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    Derek Caetano-Anolles created an article,

    ⚙️ GATK 4.3 release

    The latest GATK release came out a few weeks ago, with changes corresponding to the period of April 13, 2022 - October 13, 2022. This update brings a ton of new tools to GATK, and we highly recomm...

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    Derek Caetano-Anolles created an article,

    Introducing NVIDIA's NVScoreVariants, a new deep learning tool for filtering variants

    If you know only one thing about NVIDIA, it's probably that they manufacture popular graphics cards for computers. They started out targeting hardware to gaming machines, branding themselves as “t...

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    Derek Caetano-Anolles created an article,

    🗓️ DRAGEN-GATK Webinar [Oct. 21, 2022]

    This October 21, join us for an interactive online workshop on Whole-Genome Analysis with DRAGEN-GATK! In this webinar, you will get the opportunity to will learn what it is, why it exists, and ho...

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    Derek Caetano-Anolles created an article,

    GATK Best Practices for Structural Variation Discovery on Single Samples

    GATK-SV is a structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data. Before you begin processing, please read the full pipeline documentation available ...

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    Derek Caetano-Anolles created an article,

    Structural Variants

    Structural variants are key players in human evolution and disease, but they are difficult to discover and analyze. There are many tools out there to discover structural variants; some algorithms a...