Tutorials
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(Notebook) Intro to using Mutect2 for somatic data
In this hands-on tutorial — the Terra Workspace of which is avaialable here —... -
(How to) Install all software packages required to follow the GATK Best Practices
Objective Install all software packages required to follow the GATK Best Pra... -
(How to) Map and clean up short read sequence data efficiently
(How to) Map and clean up short read sequence data efficiently In this tut... -
(How to) Map reads to a reference with alternate contigs like GRCH38
This document was written for GATK3. Some commands or information may be out ... -
(How to) Fix a badly formatted BAM
This document was written for GATK3. Some commands or information may be out ... -
(Notebook) Concordance of NA19017 chr20 gCNV calls
This notebook shows how to perform the analysis that is alluded to in this tu... -
(How to part II) Sensitively detect copy ratio alterations and allelic segments
Document is currently under review and in BETA. It is incomplete and may cont... -
(How to) Run GATK in a Docker container
This document explains how to install and use Docker to run GATK on a local m... -
(How to) Consolidate GVCFs for joint calling with GenotypeGVCFs
In GATK4, the GenotypeGVCFs tool can only take a single input i.e., 1) a sing... -
(How to) Create a Spark cluster on Google Dataproc
As noted in our brief primer on Dataproc, there are two ways to create and co... -
(How to) Call common and rare germline copy number variants
The tutorial outlines steps in detecting germline copy number variants (gCN... -
(How to) Call somatic mutations using GATK4 Mutect2
This tutorial is applicable to Mutect2 version 4.1.1.0 and higher. Post sugge... -
Funcotator Information and Tutorial
This page explains what Funcotator is and how to run it. Table of Contents... -
(How to) Run the Pathseq pipeline
Beta tutorial Please report any issues in the comments section. Overview Pa... -
(Notebook) Correlate gCNV callset metrics and annotations
This notebook examines gCNV callset annotations using data from this tutorial... -
(How to) Run Spark-enabled GATK tools on a local multi-core machine
This is a placeholder for a document in progress. -
(How to) Install and use Conda for GATK4
Some tools in GATK4, like the gCNV pipeline and the new deep learning variant... -
(How to) Filter variants either with VQSR or by hard-filtering
This article outlines two different approaches to site-level variant filtrat... -
(How to) Run Spark-enabled GATK tools on a Spark cluster
This is a placeholder for documentation in progress. -
(How to part I) Sensitively detect copy ratio alterations and allelic segments
Document is currently under review and in BETA. It is incomplete and may cont... -
(How to) Filter on genotype using VariantFiltration
Before using VariantFiltration, please read the entirety of the discussion in... -
(How to) Call somatic mutations using GATK4 Mutect2 (Deprecated)
This tutorial is now deprecated and only valid for Mutect2 v4.1.0.0 and earli... -
(How to) Execute Workflows from the gatk-workflows Git Organization
The gatk-workflows git organization houses a set of repositories containing w...