As of May 1st 2025, GATK forums will be community-driven and self-moderated. They will not be moderated or monitored by a GATK team member. Over the years community members have used these forums to support others with their expertise. This has resulted in advice from a wide range of experts, applying GATK to many contexts.

Jul 20, 2024 · The tools can be used individually or chained together into complete workflows. We provide end-to-end workflows, called GATK Best Practices, tailored for specific use cases. Starting with version 4.0, GATK contains a copy of the Picard toolkit, so all Picard tools are available from within GATK itself.

GATK on local HPC infrastructure GATK on Alibaba Cloud See all articles FAQ Which training sets arguments should I use for running VQSR? FAQ for Mutect2 What is physical phasing? Where can I get the GATK source code? Is it open-source? Are there Best Practices for calling variants in RNAseq data? Does GATK work on non-diploid organisms? See all ...

About the GATK Best Practices This document provides important context information about how the GATK Best ... GATK Best Practices for Structural Variation Discovery on Single Samples GATK-SV is a structural variation discovery pipeline for Illumina short-read ... Mitochondrial short variant discovery (SNVs + Indels)

(How to) Run germline single sample short variant discovery in DRAGEN mode DRAGEN-GATK introduced several new changes to GATK, including two new tools, ... (How to) Generate an unmapped BAM from FASTQ or aligned BAM Objective Here we outline how to generate an unmapped BAM (uBAM) from either... (Notebook) Intro to using Mutect2 for somatic data

The GATK Best Practices provide step-by-step recommendations for performing variant discovery analysis in high-throughput sequencing (HTS) data. There are several different GATK Best Practices workflows tailored to particular applications depending on the type of variation of interest and the technology employed.

Jun 25, 2024 · Starting with version 3.6, the GATK requires Java Runtime Environment version 1.8 (Java 8). Previous versions down to 2.6 required JRE 1.7, and earlier versions required 1.6.

Jun 25, 2024 · Funcotator is a functional annotation tool in the core GATK toolset and was designed to handle both somatic and germline use cases. Funcotator reads in a VCF file, labels each variant with one of twenty-three distinct variant classifications, produces gene information (e.g. affected gene, predicted variant amino acid sequence, etc.), and ...

Troubleshooting GATK4 Issues See all articles Glossary See all articles Algorithms See all articles

Jul 24, 2024 · Starting with GATK version 3.x, a new approach was introduced, which decoupled the two internal processes that previously composed variant calling: (1) the initial per-sample collection of variant context statistics and calculation of all possible genotype likelihoods given each sample by itself, which require access to the original BAM file ...