gatk

bioinformatics dna gatk genome genomics ngs science sequencing spark

Score: 14.605698238642361

Last synced: about 8 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 (about 11 years ago)
Default Branch: master
Last Pushed: 2026-01-20T22:35:25.000Z (16 days ago)
Last Synced: 2026-01-21T00:54:28.055Z (16 days ago)
Topics: bioinformatics, dna, gatk, genome, genomics, ngs, science, sequencing, spark
Language: Java
Homepage: https://software.broadinstitute.org/gatk
Size: 466 MB
Stars: 1,898
Watchers: 155
Forks: 623
Open Issues: 1,416
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

Create event: 215
Delete event: 167
Fork event: 33
Gollum event: 2
Issue comment event: 258
Issues event: 76
Member event: 2
Pull request event: 284
Pull request review comment event: 527
Pull request review event: 585
Push event: 1287
Release event: 2
Watch event: 157
Total: 3595

Last Year

Create event: 196
Delete event: 147
Fork event: 30
Issue comment event: 216
Issues event: 70
Member event: 1
Pull request event: 249
Pull request review comment event: 361
Pull request review event: 442
Push event: 1191
Release event: 1
Watch event: 147
Total: 3051

Committers metadata

Last synced: 4 months ago

Total Commits: 3,697
Total Committers: 133
Avg Commits per committer: 27.797
Development Distribution Score (DDS): 0.864

Commits in past year: 46
Committers in past year: 21
Avg Commits per committer in past year: 2.19
Development Distribution Score (DDS) in past year: 0.674

Name	Email	Commits
Louis Bergelson	l**b@b**g	502
David Benjamin	d**n@b**g	414
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	107
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: 3 months ago

Total issues: 281
Total pull requests: 975
Average time to close issues: 5 months
Average time to close pull requests: 28 days
Total issue authors: 211
Total pull request authors: 58
Average comments per issue: 2.7
Average comments per pull request: 1.37
Merged pull request: 656
Bot issues: 0
Bot pull requests: 13

Past year issues: 69
Past year pull requests: 289
Past year average time to close issues: 14 days
Past year average time to close pull requests: 9 days
Past year issue authors: 63
Past year pull request authors: 29
Past year average comments per issue: 0.77
Past year average comments per pull request: 0.6
Past year merged pull request: 180
Past year bot issues: 0
Past year bot pull requests: 9

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/broadinstitute/gatk

Top Issue Authors

droazen (9)
GATKSupportTeam (8)
jamesemery (7)
gokalpcelik (6)
bbimber (4)
jonn-smith (4)
lbergelson (4)
gevro (4)
yurivict (4)
DarioS (3)
lovelycatZ (3)
meganshand (3)
Stikus (3)
mrymkdnz (3)
vappiah (3)

Top Pull Request Authors

mcovarr (248)
gbggrant (167)
lbergelson (74)
rsasch (72)
RoriCremer (61)
droazen (31)
koncheto-broad (29)
davidbenjamin (21)
meganshand (19)
jamesemery (19)
mwalker174 (18)
ilyasoifer (17)
cmnbroad (16)
ldgauthier (15)
dependabot[bot] (13)

Top Issue Labels

bug (13)
Funcotator (11)
GenomicsDB (6)
community-request (5)
Mutect (5)
PRIORITY_HIGH (4)
Spark (4)
HaplotypeCaller (4)
Germline CNV (4)
learn GATK (3)
Documentation (3)
Docker (2)
BuildSystem (2)
BQSR (2)
tests (2)
WaitingForUser (2)
JointCalling (2)
performance (2)
question (2)
enhancement (1)
HTSJDK (1)
Engine (1)
CNN (1)
GenotypeGVCFs (1)
DRAGEN-GATK (1)
Copy Number tools (1)
cram (1)
tools (1)
Python (1)
assembly (1)

Top Pull Request Labels

dependencies (13)
java (13)
Funcotator (1)
DRAGEN-GATK (1)
CNN (1)
enhancement (1)
HaplotypeCaller (1)
⛔ DO NOT MERGE ⛔ (1)

Package metadata

Total packages: 2
Total downloads: unknown
Total dependent packages: 2 (may contain duplicates)
Total dependent repositories: 3 (may contain duplicates)
Total versions: 83

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: 4.6.2.0 (published 10 months ago)
Last Synced: 2025-10-30T07:45:04.959Z (3 months ago)
Versions: 51
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: 4.6.2.0 (published 10 months ago)
Last Synced: 2025-10-30T07:45:14.507Z (3 months ago)
Versions: 32
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%

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

scripts/docker/gatkbase/Dockerfile docker

ubuntu 18.04 build

scripts/mitochondria_m2_wdl/Haplochecker/Dockerfile docker

java openjdk-8-jre build

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