# broadinstitute/gatk

Official code repository for GATK versions 4 and up

Repository: https://github.com/broadinstitute/gatk
Canonical: https://ross.abutalabs.com/products/gatk
Homepage: https://software.broadinstitute.org/gatk
Language: Java
License: NOASSERTION
License Family: other
Topics: genomics, spark, science, dna, ngs, sequencing, genome, bioinformatics, gatk
Last push: 2026-08-26T20:11:41+00:00

## Health v2 (maintenance only)
Score: 88/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 99, release rhythm 66, longevity 100
- inputs: {"age_days": 4292, "days_push": 7, "days_rel": 15, "gap_med": 328.0, "n_releases_24m": 3}
- flags: no_license
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1991, forks 625 (observed 2026-08-28T04:06:03.141186+00:00)

## What it is
GATK (Genome Analysis Toolkit) is the Broad Institute's industry-standard toolkit for analyzing high-throughput DNA and RNA sequencing data, with a primary focus on variant discovery and genotyping. GATK 4 unifies the GATK and Picard codebases in a streamlined Java framework, with selected tools parallelizable via Apache Spark on local clusters or the cloud.

## Use cases
- call SNPs and indels from whole-genome or exome sequencing data
- run germline variant discovery best-practices pipelines
- detect somatic mutations in tumor-normal pairs with Mutect2
- analyze copy number and structural variation from sequencing data
- process and quality-control BAM/CRAM files from Illumina sequencers
- scale variant calling across a Spark cluster or cloud platform
- analyze genomes from any organism with any ploidy level

## When to choose
- you need the industry-standard, best-practice toolchain for germline or somatic short variant calling
- you are processing exomes or whole genomes, especially from Illumina platforms
- you need reproducible, community-vetted pipelines runnable on HPC, cloud (Terra, GCP, AWS, Azure), or locally
- you want bundled Picard utilities for SAM/BAM/CRAM processing and QC

## When to avoid
- you need long-read (PacBio/ONT) variant calling, which GATK supports only partially
- you want a lightweight GUI-based genome browser or visualization tool
- your analysis is not sequencing-based (e.g., proteomics or metabolomics)
- you need a simple one-command aligner rather than a full analysis toolkit

## Facets
- artifact type: cli-tool
- maturity: active
- function: cli, developer-tools, data-science, streaming
- domain: bioinformatics, data-science
- platform: windows, cloud, jvm
- tags: genomics, variant-calling, ngs, sequencing, spark, picard, dna, bioinformatics, java, high-performance-computing, linux, macos, docker

## Member repositories
- broadinstitute/gatk (main) score 88

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:06:03.141186+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T03:02:40.613839+00:00, confidence not recorded.
  - readme: https://github.com/broadinstitute/gatk (fetched 2026-08-28T04:06:03.141186+00:00, sha 4fab3cddc648)
  - homepage: https://software.broadinstitute.org/gatk (fetched 2026-08-29T10:42:36.320670+00:00, sha b850e8ee2bf1)
  - site_page: https://gatk.broadinstitute.org/hc/en-us/articles/360045944831 (fetched 2026-08-29T10:42:36.325563+00:00, sha 8bcdce20e3be)
  - site_page: https://gatk.broadinstitute.org/hc/categories/360002369672 (fetched 2026-08-29T10:42:36.329120+00:00, sha 4775cf8d8df9)
  - site_page: https://gatk.broadinstitute.org/hc/articles/360035889771 (fetched 2026-08-29T10:42:36.327343+00:00, sha 1e9f42a8666b)
  - site_page: https://gatk.broadinstitute.org/hc/categories/360002310591 (fetched 2026-08-29T10:42:36.323397+00:00, sha 27243aac44a0)
- Data as of 2026-08-30T08:39:29.467469+00:00.