Derek Caetano-Anolles
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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...
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🗓️ 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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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 ...
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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...
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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...
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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...
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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...
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Evaluating the quality of a germline short variant callset
The germline short variant discovery pipeline produces a variant callset in the form of a VCF file. So what’s next? Technically, that callset is ready to be used in downstream analysis. But before ...
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Somatic calling is NOT simply a difference between two callsets
To better understand what somatic calling entails, we contrast it to germline calling. We delve into the technical details of what is the same and what is different between Mutect2 and HaplotypeCal...
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Hard-filtering germline short variants
This document aims to provide some insight into the logic of the generic hard-filtering recommendations that we provide as a substitute for VQSR (the method we normally recommend for filtering germ...