vcf-kit
VCF-kit: Assorted utilities for the variant call format
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
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary
Keywords
Repository
VCF-kit: Assorted utilities for the variant call format
Basic Info
- Host: GitHub
- Owner: AndersenLab
- License: mit
- Language: Python
- Default Branch: master
- Homepage: http://www.andersenlab.org
- Size: 11 MB
Statistics
- Stars: 131
- Watchers: 17
- Forks: 26
- Open Issues: 19
- Releases: 17
Topics
Metadata Files
README.md
VCF-kit - Documentation
VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files. A summary of the commands is provided below.
| Command |Description | |:----------|------------------------------------------------------------------------------------------| | calc | Obtain frequency/count of genotypes and alleles. | | call | Compare variants identified from sequences obtained through alternative methods against a VCF. | | filter | Filter variants with a minimum or maximum number of REF, HET, ALT, or missing calls. | | geno | Various operations at the genotype level. | | genome | Reference genome processing and management. | | hmm | Hidden-markov model for use in imputing genotypes from parental genotypes in linkage studies. | | phylo | Generate dendrograms from a VCF. | | primer | Generate primers for variant validation. | | rename | Add a prefix, suffix, or substitute a string in sample names. | | tajima | Calculate Tajima’s D. | | vcf2tsv | Convert a VCF to TSV. |
Installation
VCF-Kit has been upgraded to Python 3
VCF-kit has been tested with Python 3.10. VCF-kit makes use of additional software for a variety of tasks:
- bwa (v 0.7.12)
- samtools (v 1.3)
- bcftools (v 1.3)
- blast (v 2.2.31+)
- primer3 (v 2.5.0)
You can install these dependencies and VCF-kit using conda, or you can use a Docker image.
Conda
```bash conda config --add channels bioconda conda config --add channels conda-forge conda create -n vcf-kit \ danielecook::vcf-kit=0.2.6 \ "bwa>=0.7.17" \ "samtools>=1.10" \ "bcftools>=1.10" \ "blast>=2.2.31" \ "primer3>=2.5.0"
conda activate vcf-kit ```
Docker
You can also run VCF-kit with all installed dependencies using docker:
bash
docker run -it andersenlab/vcf-kit vk
Owner
- Name: Andersen Lab
- Login: AndersenLab
- Kind: organization
- Email: erik.andersen@northwestern.edu
- Location: Chicago
- Repositories: 167
- Profile: https://github.com/AndersenLab
Northwestern University
GitHub Events
Total
- Issues event: 6
- Watch event: 11
- Issue comment event: 7
- Push event: 6
- Pull request event: 4
- Fork event: 2
Last Year
- Issues event: 6
- Watch event: 11
- Issue comment event: 7
- Push event: 6
- Pull request event: 4
- Fork event: 2
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 619
- Total Committers: 4
- Avg Commits per committer: 154.75
- Development Distribution Score (DDS): 0.032
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel Cook | d****k@g****m | 599 |
| Daniel E Cook | D****k@g****m | 18 |
| Daniel E. Cook | d****1@q****u | 1 |
| Daniel E. Cook | d****1@q****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 49
- Total pull requests: 3
- Average time to close issues: 7 months
- Average time to close pull requests: 10 months
- Total issue authors: 46
- Total pull request authors: 3
- Average comments per issue: 2.9
- Average comments per pull request: 0.33
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 1
- Average time to close issues: about 20 hours
- Average time to close pull requests: 5 days
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.67
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- nuin (2)
- andreyurch (2)
- mauri101-Ar (2)
- boutrys (1)
- amykwebster (1)
- sofsta (1)
- mariesaitou (1)
- shanmugavadivelps (1)
- JieGao-XTBG (1)
- asherichia (1)
- hoyonh (1)
- ccastane9 (1)
- AlexWanghaoming (1)
- aozalevsky (1)
- selasphoruskershaw (1)
Pull Request Authors
- mauri101-Ar (1)
- samwachspress (1)
- danielecook (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 153 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 17
- Total maintainers: 2
pypi.org: vcf-kit
Assorted utilities for the variant call format
- Homepage: https://www.github.com/andersenlab/vcf-kit
- Documentation: https://vcf-kit.readthedocs.io/en/latest/?badge=latest
- License: MIT
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Latest release: 0.2.9
published about 5 years ago
Rankings
Maintainers (1)
spack.io: py-vcf-kit
VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.
- Homepage: https://github.com/AndersenLab/VCF-kit
- License: []
-
Latest release: 0.1.6
published almost 4 years ago
Rankings
Maintainers (1)
Dependencies
- awesome-slugify *
- biopython *
- clint *
- cython *
- cyvcf2 *
- docopt *
- intervaltree *
- jinja2 *
- logzero *
- matplotlib *
- networkx *
- numpy *
- pomegranate *
- pytest *
- pytest-runner *
- requests *
- scipy *
- setuptools *
- tabulate *
- actions/checkout v2 composite
- actions/create-release v1 composite
- actions/upload-artifact v2 composite
- conda-incubator/setup-miniconda v2 composite
- pypa/gh-action-pypi-publish master composite
- actions/checkout v2 composite
- elgohr/Publish-Docker-Github-Action master composite
- continuumio/miniconda3 4.8.2 build