https://github.com/broadinstitute/gatk-sv
A structural variation pipeline for short-read sequencing
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
9 of 20 committers (45.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary
Keywords
bioinformatics
genomics
structural-variants
structural-variation
Keywords from Contributors
genome
dna
gatk
ngs
sequencing
wdl
Last synced: 5 months ago
·
JSON representation
Repository
A structural variation pipeline for short-read sequencing
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://broadinstitute.github.io/gatk-sv/
- Size: 88.8 MB
Statistics
- Stars: 193
- Watchers: 13
- Forks: 77
- Open Issues: 121
- Releases: 78
Topics
bioinformatics
genomics
structural-variants
structural-variation
Created over 5 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Contributing
License
Code of conduct
README.md
GATK-SV
A structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data.
For technical documentation on GATK-SV, including how to run the pipeline, please refer to our website.
Repository structure
/dockerfiles: Resources for building pipeline docker images/inputs: files for generating workflow inputs/templates: Input json file templates/values: Input values used to populate templates
/scripts: scripts for running tests, building dockers, and analyzing cromwell metadata files/src: main pipeline scripts/RdTest: scripts for depth testing/sv-pipeline: various scripts and packages used throughout the pipeline/svqc: Python module for checking that pipeline metrics fall within acceptable limits/svtest: Python module for generating various summary metrics from module outputs/svtk: Python module of tools for SV-related datafile parsing and analysis/WGD: whole-genome dosage score scripts
/wdl: WDLs running the pipeline. There is a master WDL for running each module, e.g.ClusterBatch.wdl./website: website code
CI/CD
This repository is maintained following the norms of
continuous integration (CI) and continuous delivery (CD).
GATK-SV CI/CD is developed as a set of Github Actions
workflows that are available under the .github/workflows
directory. Please refer to the workflow's README
for their current coverage and setup.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Vahid | V****i | 123 |
| epiercehoffman | e****h@b****g | 117 |
| Mark Walker | m****w@b****g | 95 |
| gatk-sv-bot | 1****t | 84 |
| cwhelan | c****n@b****g | 33 |
| Karan Jaisingh | k****g@b****g | 23 |
| TedBrookings | t****s@g****m | 18 |
| kirtanav98 | 1****8 | 13 |
| tedsharpe | t****e | 10 |
| Ryan L. Collins | r****s@g****u | 10 |
| Shadi Zaheri | 7****i | 8 |
| henriqueribeiro | h****o | 7 |
| Snow | x****o@u****u | 4 |
| Justin Lim | j****1@m****u | 4 |
| Matt Welland | m****e@g****m | 2 |
| Michael Franklin | m****n@p****g | 1 |
| Nick Watts | n****s@b****g | 1 |
| Peter Diakumis | p****s@g****m | 1 |
| Stephanie Hao | s****o@m****u | 1 |
| knathamuni | 1****i | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 125
- Total pull requests: 271
- Average time to close issues: about 1 year
- Average time to close pull requests: about 1 month
- Total issue authors: 40
- Total pull request authors: 18
- Average comments per issue: 1.31
- Average comments per pull request: 0.49
- Merged pull requests: 163
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 23
- Pull requests: 144
- Average time to close issues: about 1 month
- Average time to close pull requests: 9 days
- Issue authors: 13
- Pull request authors: 10
- Average comments per issue: 0.61
- Average comments per pull request: 0.26
- Merged pull requests: 76
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mwalker174 (28)
- epiercehoffman (23)
- cwhelan (9)
- MattWellie (7)
- NewOrange (4)
- CuriousTim (3)
- boboppie (3)
- sdwang008 (3)
- henriqueribeiro (3)
- TedBrookings (2)
- cccnrc (2)
- c2997108 (2)
- levinyi (2)
- hab45 (2)
- RCollins13 (2)
Pull Request Authors
- epiercehoffman (57)
- kjaisingh (50)
- VJalili (49)
- mwalker174 (40)
- cwhelan (20)
- CuriousTim (13)
- knathamuni (9)
- xuefzhao (6)
- kirtanav98 (6)
- TedBrookings (4)
- zhangting1991 (4)
- RCollins13 (3)
- MattWellie (3)
- shadizaheri (2)
- lmtani (2)
Top Labels
Issue Labels
enhancement (5)
bug (5)
low priority (4)
low effort (3)
docker (2)
question (1)
medium priority (1)
high effort (1)
medium effort (1)
optimization (1)
duplicate (1)
Pull Request Labels
bug (17)
enhancement (14)
documentation (7)
docker (3)
testing (2)
optimization (1)
methods (1)