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vcftoolz

vcftoolz: a Python package for comparing and evaluating Variant Call Format files. - Published in JOSS (2019)

https://github.com/cfsan-biostatistics/vcftoolz

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

Tools for working with Variant Call Format files.

Basic Info
  • Host: GitHub
  • Owner: CFSAN-Biostatistics
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 281 KB
Statistics
  • Stars: 12
  • Watchers: 6
  • Forks: 5
  • Open Issues: 7
  • Releases: 0
Created over 7 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Authors

README.rst 

===============================
VCF Toolz
===============================


.. Image showing the PyPI version badge - links to PyPI
.. image:: https://img.shields.io/pypi/v/vcftoolz.svg
        :target: https://pypi.python.org/pypi/vcftoolz

.. Image showing the Travis Continuous Integration test status, commented out for now
.. .. image:: https://img.shields.io/travis/CFSAN-Biostatistics/vcftoolz.svg
..        :target: https://travis-ci.org/CFSAN-Biostatistics/vcftoolz

.. Image showing the JOSS paper badge
.. image:: http://joss.theoj.org/papers/10.21105/joss.01144/status.svg
   :target: https://doi.org/10.21105/joss.01144

Tools for working with Variant Call Format files.

VCF Toolz was developed by the United States Food
and Drug Administration, Center for Food Safety and Applied Nutrition.

* Free software
* Documentation: https://vcftoolz.readthedocs.io
* Source Code: https://github.com/CFSAN-Biostatistics/vcftoolz
* PyPI Distribution: https://pypi.python.org/pypi/vcftoolz


Features
--------

* Compares the snps in two or more VCF files.
* Lists the snps that are unique to each VCF file with full genotype information per snp.
* Lists the snps that are missing from each VCF file if present in at least two other VCF files.
* Generates Venn diagrams of positions and snps in the VCF files.
* Reports precision, recall, and F1 score when the truth is known.
* Reports the effectiveness of filtered variants when the truth is known.
* Reformat the VCF file in a tall-narrow format for easy viewing and diffs.
* Count samples, positions, calls, snps, indels, other variants, missing calls, and filter reasons.
* Plot calls along the length of the genome and show the location of filtered calls.


Citing VCF Toolz
--------------------------------------

To cite VCF Toolz, please reference the VCF Toolz paper:

    https://doi.org/10.21105/joss.01144


License
-------

See the LICENSE file included in the VCF Toolz distribution.

Owner

  • Name: CFSAN (Center for Food Safety and Applied Nutrition)
  • Login: CFSAN-Biostatistics
  • Kind: organization

JOSS Publication

vcftoolz: a Python package for comparing and evaluating Variant Call Format files.
Published
March 26, 2019
DOI
Volume 4, Issue 35, Page 1144
Authors
Steve Davis ORCID
U.S. Food and Drug Administration
Editor
Melissa Gymrek ORCID
Tags
bioinformatics next-generation sequencing variant call format VCF
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 1
  • Fork event: 3
Last Year
  • Watch event: 1
  • Fork event: 3

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 85
  • Total Committers: 2
  • Avg Commits per committer: 42.5
  • Development Distribution Score (DDS): 0.129
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Steve Davis s****s@f****v 74
Justin Payne c****g@g****m 11
Committer Domains (Top 20 + Academic)
fda.hhs.gov: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 13
  • Total pull requests: 2
  • Average time to close issues: 2 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 11
  • Total pull request authors: 2
  • Average comments per issue: 1.62
  • Average comments per pull request: 0.5
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 months
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pablosolar (2)
  • manimino (2)
  • Kaskere (1)
  • splaisan (1)
  • denise0593 (1)
  • ulloaa (1)
  • mbyott (1)
  • 512714 (1)
  • simeonhebrew (1)
  • SiripongT (1)
  • sarakn97 (1)
Pull Request Authors
  • jsquaredosquared (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 62 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 2
pypi.org: vcftoolz

Tools for working with Variant Call Format files.

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 62 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 16.8%
Average: 18.8%
Stargazers count: 20.3%
Dependent repos count: 21.6%
Downloads: 25.1%
Maintainers (2)
stevendavis crashfrog
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • wheel ==0.23.0
setup.py pypi