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Derek Caetano-Anolles

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  • Phred-scaled quality scores

    You may have noticed that a lot of the scores that are output by the GATK are in Phred scale. The Phred scale was originally used to represent base quality scores emitted by the Phred program in th...

  • (How to) Call rare germline copy number variants

    The tutorial outlines steps in detecting germline copy number variants (gCNVs) and illustrates two workflow modes--cohort mode and case mode. The cohort mode simultaneously generates a cohort mode...

  • 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, ...

  • Intervals and interval lists

    Interval lists define subsets of genomic regions, sometimes even just individual positions in the genome. You can provide GATK tools with intervals or lists of intervals when you want to restrict t...

  • 🗓️ 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...

  • FAQ for Mutect2

    Here is a collection of questions related to Mutect2 that we frequently find asked on our GATK forum. For more info on the Mutect2 tool, visit the Mutect2 tool index. For more info on the Mutect2 ...

  • Resource bundle

    The GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. We provide several versions of the bundle corresponding to the various reference b...

  • Coverage - Read depth metrics

    Coverage (a.k.a. read depth) describes the amount of sequence data that is available per position in the sequenced genome territory. Coverage in overall sequence quality metrics This documentatio...

  • Funcotator Annotation Specifications

    Introduction This page details the specification of the annotations that Funcotator can create. Detailed information on Funcotator can be found in this forum post. Table of Contents Introd...

  • HDF5 format

    A number of GATK tools produce or take in HDF5 format data (1; 2), e.g. CollectReadCounts and CreateReadCountPanelOfNormals in the CNV workflow. Some tools like CollectReadCounts also allow for wr...