broadinstitute/gatk
Official code repository for GATK versions 4 and up observed · 2026-08-28
Health v2 · maintenance only
88/100
- Activity 99
- Release rhythm 66
- Longevity 100
Flags: no_license
How is this computed?
round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10) — computed 2026-09-03. Adoption (stars, forks) is never an input.
- gap_med: 328.0
- age_days: 4292
- days_rel: 15
- days_push: 7
- n_releases_24m: 3
Adoption not part of the score
1991 stars · 625 forks observed · 2026-08-28
What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded
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
cli-tool · maturity active
cli developer-tools data-science streaming bioinformatics data-science windows cloud jvm genomics variant-calling ngs sequencing spark picard dna bioinformatics java high-performance-computing linux macos docker
6 sources
- readme: https://github.com/broadinstitute/gatk · fetched 2026-08-28 · 4fab3cddc648
- homepage: https://software.broadinstitute.org/gatk · fetched 2026-08-29 · b850e8ee2bf1
- site_page: https://gatk.broadinstitute.org/hc/en-us/articles/360045944831 · fetched 2026-08-29 · 8bcdce20e3be
- site_page: https://gatk.broadinstitute.org/hc/categories/360002369672 · fetched 2026-08-29 · 4775cf8d8df9
- site_page: https://gatk.broadinstitute.org/hc/articles/360035889771 · fetched 2026-08-29 · 1e9f42a8666b
- site_page: https://gatk.broadinstitute.org/hc/categories/360002310591 · fetched 2026-08-29 · 27243aac44a0
Member repositories
| Repository | Role | Health v2 |
|---|---|---|
| broadinstitute/gatk | main | 88 |
For agents
markdown · JSON · MCP: product_card(name="broadinstitute/gatk")
Data as of 2026-08-30T08:39:29.467469+00:00 · Report a problem