gatk

Wide variety of tools with a primary focus on variant discovery and genotyping

Apache-2.0 gatk.broadinstitute.org gatk 8 releases newest changed 13 days ago

version4.7.0.0 attributegatk rev34ca302a9572963c02e385c056be37c85ff51b77 2026-09-24 · one commit for every system systems✓ aarch64-darwin✓ aarch64-linuxx86_64-darwin✓ x86_64-linux

$ devbox add gatk@4.7.0.0

$ nix shell github:NixOS/nixpkgs/34ca302a9572963c02e385c056be37c85ff51b77#gatk

JSON: /v2/resolve?name=gatk&version=latest

Releases

newest first, as /v2/pkg orders them

Version	arm mac	arm linux	x86 mac	x86 linux	Attribute	Commit	Date
4.7.0.0resolved	✓	✓	–	✓	`gatk`	02f5696b0e	2026-09-13
4.6.2.0	✓	✓	✓	✓	`gatk`	varies	2026-08-27
4.6.1.0	✓	✓	✓	✓	`gatk`	ebe4301cbd	2025-04-17
4.6.0.0	✓	✓	✓	✓	`gatk`	4ae2e64753	2024-11-03
4.5.0.0	✓	✓	✓	✓	`gatk`	a9858885e1	2024-06-12
4.4.0.0	✓	✓	✓	✓	`gatk`	fd04bea4cb	2023-12-13
4.3.0.0	✓	✓	✓	✓	`gatk`	194c2aa446	2023-03-16
4.2.6.1	✓	✓	✓	✓	`gatk`	varies	2022-10-13

Prereleases are listed but latest never picks one. “varies” means each system last changed at a different nixpkgs commit — the release page lists them.

Description

The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit. These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs. And although it was originally developed for human genetics, the GATK has since evolved to handle genome data from any organism, with any level of ploidy.