Critical open source scientific software: https://github.com/broadinstitute/gatk
bioinformatics dna gatk genome genomics ngs science sequencing spark
Score: 30.38384942585074
Last synced: about 21 hours ago
JSON representation
Repository metadata:
Official code repository for GATK versions 4 and up
- Host: GitHub
- URL: https://github.com/broadinstitute/gatk
- Owner: broadinstitute
- License: other
- Created: 2014-12-02T20:50:36.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2026-11-04T23:10:13.000Z (9 days ago)
- Last Synced: 2026-11-04T23:14:32.319Z (9 days ago)
- Topics: bioinformatics, dna, gatk, genome, genomics, ngs, science, sequencing, spark
- Language: Java
- Homepage: https://software.broadinstitute.org/gatk
- Size: 471 MB
- Stars: 2,010
- Watchers: 155
- Forks: 631
- Open Issues: 1,464
-
Metadata Files:
- Readme: README.md
- License: LICENSE.TXT
- Code of conduct: CODE_OF_CONDUCT.md
- Authors: AUTHORS
Owner metadata:
- Name: Broad Institute
- Login: broadinstitute
- Email:
- Kind: organization
- Description: Broad Institute of MIT and Harvard
- Website: http://www.broadinstitute.org/
- Location: Cambridge, MA
- Twitter: broadinstitute
- Company:
- Icon url: https://avatars.githubusercontent.com/u/393552?v=4
- Repositories: 1083
- Last Synced at: 2023-04-09T09:48:11.262Z
- Profile URL: https://github.com/broadinstitute
GitHub Events
Total
- Commit comment event: 1
- Create event: 259
- Delete event: 188
- Fork event: 37
- Gollum event: 2
- Issue comment event: 306
- Issues event: 80
- Member event: 2
- Pull request event: 313
- Pull request review comment event: 556
- Pull request review event: 622
- Push event: 1706
- Release event: 2
- Watch event: 177
- Total: 4251
Last Year
- Commit comment event: 1
- Create event: 53
- Delete event: 24
- Fork event: 4
- Issue comment event: 50
- Issues event: 4
- Pull request event: 32
- Pull request review comment event: 33
- Pull request review event: 44
- Push event: 453
- Watch event: 22
- Total: 720
Committers metadata
Last synced: 2 days ago
Total Commits: 3,707
Total Committers: 133
Avg Commits per committer: 27.872
Development Distribution Score (DDS): 0.865
Commits in past year: 10
Committers in past year: 5
Avg Commits per committer in past year: 2.0
Development Distribution Score (DDS) in past year: 0.7
| Name | Commits | |
|---|---|---|
| Louis Bergelson | l****b@b****g | 502 |
| David Benjamin | d****n@b****g | 417 |
| Adam Kiezun | a****n@g****m | 298 |
| Chris Norman | c****n@b****g | 254 |
| droazen | d****n@b****g | 238 |
| jamesemery | e****j@b****g | 170 |
| samuelklee | s****e | 168 |
| lichtens | l****s@b****g | 139 |
| Tom White | t****e@g****m | 119 |
| Jonn Smith | j****h | 110 |
| ldgauthier | g****r@b****g | 98 |
| Steve Huang | s****g@b****g | 90 |
| JP Martin | j****n@g****m | 80 |
| sooheelee | s****e@b****g | 66 |
| tedsharpe | t****e | 59 |
| Daniel Gómez-Sánchez | m****S | 58 |
| Mark Walker | m****w@b****g | 56 |
| meganshand | m****d@b****g | 51 |
| Takuto Sato | t****o@b****g | 47 |
| vruano | v****o@g****m | 43 |
| cwhelan | c****n@g****m | 35 |
| achevali | a****c@b****g | 29 |
| Ron Levine | r****e@b****g | 28 |
| Andrey Smirnov | a****9@g****m | 27 |
| Valentin Ruano Rubio | v****n@b****g | 27 |
| Mehrtash Babadi | m****h@b****g | 25 |
| Nalini Ganapati | 3****s | 24 |
| David Adams | d****a@g****m | 21 |
| chandrans | s****a@b****g | 21 |
| Ilya Soifer | i****r@u****m | 17 |
| and 103 more... | ||
Issue and Pull Request metadata
Last synced: 2 days ago
Total issues: 294
Total pull requests: 1,095
Average time to close issues: 6 months
Average time to close pull requests: about 1 month
Total issue authors: 221
Total pull request authors: 69
Average comments per issue: 2.62
Average comments per pull request: 1.47
Merged pull request: 720
Bot issues: 0
Bot pull requests: 15
Past year issues: 11
Past year pull requests: 112
Past year average time to close issues: N/A
Past year average time to close pull requests: 12 days
Past year issue authors: 11
Past year pull request authors: 20
Past year average comments per issue: 0.09
Past year average comments per pull request: 2.28
Past year merged pull request: 62
Past year bot issues: 0
Past year bot pull requests: 1
Top Issue Authors
- droazen (9)
- GATKSupportTeam (8)
- jamesemery (7)
- gokalpcelik (6)
- jonn-smith (5)
- gevro (4)
- lbergelson (4)
- DarioS (4)
- bbimber (4)
- yurivict (4)
- vappiah (3)
- mrymkdnz (3)
- meganshand (3)
- lovelycatZ (3)
- Stikus (3)
Top Pull Request Authors
- mcovarr (290)
- gbggrant (170)
- lbergelson (74)
- rsasch (72)
- RoriCremer (61)
- koncheto-broad (41)
- droazen (31)
- davidbenjamin (30)
- nalinigans (28)
- jamesemery (19)
- meganshand (19)
- mwalker174 (18)
- ilyasoifer (18)
- cmnbroad (16)
- dependabot[bot] (15)
Top Issue Labels
- bug (13)
- Funcotator (11)
- Mutect (6)
- GenomicsDB (6)
- community-request (5)
- Spark (4)
- PRIORITY_HIGH (4)
- HaplotypeCaller (4)
- Germline CNV (4)
- Documentation (3)
- learn GATK (3)
- performance (3)
- tests (2)
- BQSR (2)
- BuildSystem (2)
- JointCalling (2)
- Docker (2)
- WaitingForUser (2)
- question (2)
- GenotypeGVCFs (1)
- azure (1)
- Barclay (1)
- Engine (1)
- CNN (1)
- HaplotypeCallerSpark (1)
- tools (1)
- cram (1)
- wdl (1)
- PRIORITY_LOW (1)
- FlowBasedGATK (1)
Top Pull Request Labels
- dependencies (15)
- java (15)
- CNN (1)
- ⛔ DO NOT MERGE ⛔ (1)
- HaplotypeCaller (1)
- docker-refresh-not-needed (1)
- DRAGEN-GATK (1)
- SV (1)
- enhancement (1)
- documentation (1)
- Funcotator (1)
Package metadata
- Total packages: 8
-
Total downloads:
- cran: 372 last-month
- Total docker downloads: 33,950,863
- Total dependent packages: 2 (may contain duplicates)
- Total dependent repositories: 3 (may contain duplicates)
- Total versions: 93
- Total maintainers: 1
proxy.golang.org: github.com/broadInstitute/gatk
- Homepage:
- Status: removed
- Documentation: https://pkg.go.dev/github.com/broadInstitute/gatk#section-documentation
- Licenses: other
- Latest release: v0.0.0-20260818022010-0cde69eed303 (published 3 months ago)
- Last Synced: 2026-11-11T21:04:26.784Z (2 days ago)
- Versions: 1
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
- Dependent packages count: 4.262%
- Average: 4.408%
- Dependent repos count: 4.553%
proxy.golang.org: github.com/BroadInstitute/gatk
- Homepage:
- Status: removed
- Documentation: https://pkg.go.dev/github.com/BroadInstitute/gatk#section-documentation
- Licenses: other
- Latest release: v0.0.0-20260818022010-0cde69eed303 (published 3 months ago)
- Last Synced: 2026-11-11T21:04:22.732Z (2 days ago)
- Versions: 1
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
- Dependent packages count: 4.262%
- Average: 4.408%
- Dependent repos count: 4.553%
proxy.golang.org: github.com/BROADInstitute/gatk
- Homepage:
- Status: removed
- Documentation: https://pkg.go.dev/github.com/BROADInstitute/gatk#section-documentation
- Licenses: other
- Latest release: v0.0.0-20260818022010-0cde69eed303 (published 3 months ago)
- Last Synced: 2026-11-11T21:03:29.678Z (2 days ago)
- Versions: 1
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
- Dependent packages count: 4.432%
- Average: 4.581%
- Dependent repos count: 4.73%
proxy.golang.org: github.com/broadinstitute/gatk
- Homepage:
- Status: removed
- Documentation: https://pkg.go.dev/github.com/broadinstitute/gatk#section-documentation
- Licenses: other
- Latest release: v0.0.0-20250413170655-76edc75c2650 (published over 1 year ago)
- Last Synced: 2026-11-11T21:04:22.437Z (2 days ago)
- Versions: 1
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
- Dependent packages count: 4.482%
- Average: 4.633%
- Dependent repos count: 4.783%
repo1.maven.org: org.broadinstitute:gatk
Development on GATK 4
- Homepage: https://github.com/broadinstitute/gatk
- Documentation: https://appdoc.app/artifact/org.broadinstitute/gatk/
- Licenses: Apache 2.0
- Latest release: 4.7.0.0 (published 3 months ago)
- Last Synced: 2026-11-11T21:03:53.994Z (2 days ago)
- Versions: 52
- Dependent Packages: 2
- Dependent Repositories: 3
-
Rankings:
- Forks count: 8.176%
- Stargazers count: 9.934%
- Average: 13.762%
- Dependent repos count: 13.781%
- Dependent packages count: 23.158%
repo1.maven.org: org.broadinstitute:gatk-test-utils
Development on GATK 4
- Homepage: https://github.com/broadinstitute/gatk
- Documentation: https://appdoc.app/artifact/org.broadinstitute/gatk-test-utils/
- Licenses: Apache 2.0
- Latest release: 4.7.0.0 (published 3 months ago)
- Last Synced: 2026-11-11T21:04:08.231Z (2 days ago)
- Versions: 33
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
- Forks count: 6.42%
- Stargazers count: 7.765%
- Average: 23.756%
- Dependent repos count: 31.98%
- Dependent packages count: 48.86%
cran.r-project.org: gsalib
Utility Functions for 'GATK'
- Homepage: https://gatk.broadinstitute.org/hc/en-us
- Documentation: http://cran.r-project.org/web/packages/gsalib/gsalib.pdf
- Licenses: MIT + file LICENSE
- Latest release: 2.2.1 (published about 4 years ago)
- Last Synced: 2026-11-11T21:04:18.471Z (2 days ago)
- Versions: 3
- Dependent Packages: 0
- Dependent Repositories: 0
- Downloads: 372 Last month
- Docker Downloads: 33,950,863
-
Rankings:
- Forks count: 17.77%
- Stargazers count: 21.054%
- Downloads: 23.428%
- Average: 25.501%
- Dependent packages count: 29.797%
- Dependent repos count: 35.455%
- Maintainers (1)
proxy.golang.org: github.com/Broadinstitute/gatk
- Homepage:
- Status: removed
- Documentation: https://pkg.go.dev/github.com/Broadinstitute/gatk#section-documentation
- Licenses: other
- Latest release: v0.0.0-20260818022010-0cde69eed303 (published 3 months ago)
- Last Synced: 2026-11-11T21:03:54.141Z (2 days ago)
- Versions: 1
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
Dependencies
build.gradle
maven
- com.esotericsoftware:kryo 3.0.3 implementation
- com.fasterxml.jackson.module:jackson-module-scala_ * implementation
- com.github.jsr203hadoop:jsr203hadoop 1.0.3 implementation
- com.google.cloud.bigdataoss:gcs-connector 1.9.4-hadoop3 implementation
- com.google.cloud:google-cloud-bigquerystorage 2.9.1 implementation
- com.intel.gkl:gkl 0.8.8 implementation
- com.opencsv:opencsv 3.4 implementation
- com.thoughtworks.paranamer:paranamer 2.8 implementation
- commons-beanutils:commons-beanutils 1.9.3 implementation
- commons-io:commons-io 2.5 implementation
- de.javakaffee:kryo-serializers 0.41 implementation
- gov.nist.math.jama:gov.nist.math.jama 1.1.1 implementation
- it.unimi.dsi:fastutil 7.0.6 implementation
- net.grey-panther:natural-comparator 1.1 implementation
- org.aeonbits.owner:owner 1.0.9 implementation
- org.apache.commons:commons-collections4 4.1 implementation
- org.apache.commons:commons-configuration2 2.4 implementation
- org.apache.commons:commons-lang3 3.5 implementation
- org.apache.commons:commons-math3 3.5 implementation
- org.apache.commons:commons-vfs2 2.0 implementation
- org.apache.httpcomponents:httpclient 4.5.12 implementation
- org.apache.spark:spark-mllib_ * implementation
- org.bdgenomics.adam:adam-core-spark2_ * implementation
- org.bdgenomics.bdg-formats:bdg-formats 0.5.0 implementation
- org.broadinstitute:gatk-bwamem-jni 1.0.4 implementation
- org.broadinstitute:gatk-fermilite-jni 1.2.0 implementation
- org.broadinstitute:gatk-native-bindings 1.0.0 implementation
- org.broadinstitute:hdf5-java-bindings 1.1.0-hdf5_2.11.0 implementation
- org.broadinstitute:http-nio 0.1.0-rc1 implementation
- org.jgrapht:jgrapht-core 1.1.0 implementation
- org.jgrapht:jgrapht-io 1.1.0 implementation
- org.objenesis:objenesis 1.2 implementation
- org.ojalgo:ojalgo 44.0.0 implementation
- org.ojalgo:ojalgo-commons-math3 1.0.0 implementation
- org.reflections:reflections 0.9.10 implementation
- org.xerial:sqlite-jdbc 3.36.0.3 implementation
- com.google.jimfs:jimfs 1.1 testImplementation
- org.mockito:mockito-core 2.28.2 testImplementation
- org.objenesis:objenesis 2.1 testImplementation
.github/actions/upload-gatk-test-results/action.yml
actions
- actions/upload-artifact v2 composite
.github/workflows/carrot_run_test_from_pr_comment.yml
actions
- broadinstitute/carrot-publish-github-action 0.6.0 composite
.github/workflows/gatk-nightly-docker.yml
actions
- actions/checkout v2 composite
- docker/build-push-action ad44023a93711e3deb337508980b4b5e9bcdc5dc composite
- docker/login-action f054a8b539a109f9f41c372932f1ae047eff08c9 composite
- docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
.github/workflows/gatk-tests.yml
actions
- ./.github/actions/install-cromwell * composite
- ./.github/actions/upload-gatk-test-results * composite
- actions/checkout v2 composite
- actions/download-artifact v2 composite
- actions/setup-java v2 composite
- actions/upload-artifact v2 composite
- docker/build-push-action ad44023a93711e3deb337508980b4b5e9bcdc5dc composite
- docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
- docker/setup-buildx-action v1 composite
- google-github-actions/auth v0 composite
- google-github-actions/setup-gcloud v0 composite
Dockerfile
docker
- broadinstitute/gatk gatkbase-2.3.0 build
.github/actions/install-cromwell/action.yml
actions
.github/workflows/dependency_submission.yml
actions
- actions/checkout v4 composite
- actions/setup-java v4 composite
- gradle/actions/dependency-submission v4 composite
.github/actions/purge-runner-disk/action.yml
actions
scripts/docker/gatkbase/Dockerfile
docker
- ubuntu 22.04 build
scripts/mitochondria_m2_wdl/Haplochecker/Dockerfile
docker
- java openjdk-8-jre build
src/main/python/org/broadinstitute/hellbender/setup.py
pypi