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varifier

Variant call verification

https://github.com/iqbal-lab-org/varifier

Science Score: 39.0%

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 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Variant call verification

Basic Info
  • Host: GitHub
  • Owner: iqbal-lab-org
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 346 KB
Statistics
  • Stars: 16
  • Watchers: 5
  • Forks: 3
  • Open Issues: 7
  • Releases: 5
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

varifier

Note: full documentation is under construction.

If you use Varifier, please cite: https://doi.org/10.1186/s13059-022-02714-x

Installation

conda

Conda (channel only) bioconda version

Prerequisite: conda (and bioconda channel correctly set up)

shell $ conda install varifier

Container

Docker images are hosted at quay.io.

singularity

Prerequisite: singularity

shell $ URI="docker://quay.io/iqballab/varifier" $ singularity exec "$URI" varifier --help

The above will use the latest version. If you want to specify a version/commit then use a tag (or commit) like so.

shell $ TAG="3c8152a" $ URI="docker://quay.io/iqballab/varifier:${TAG}"

docker

Docker Repository on Quay

Prerequisite: docker

shhell $ docker pull quay.io/iqballab/varifier $ docker run quay.io/iqballab/varifier varifier --help

You can find all the available tags on the quay.io repository.

Local

Dependencies:

  • Python 3 (tested on version 3.6.9)
  • mummer installed
  • paftools.js and k8 in your path. See https://github.com/lh3/minimap2/tree/master/misc

Install:

pip3 install .

Usage

To verify calls in a VCF file, you will need:

  1. test.vcf - the VCF file to be tested
  2. ref.fasta - FASTA file of reference corresponding to the VCF file
  3. truth.fasta - a truth genome FASTA file

Run: varifier vcf_eval truth.fasta ref.fasta test.vcf out_dir

This makes a new directory called out_dir. The results are in the file summary_stats.json.

Tests

To run the tests, run tox from the root of the repository.

Owner

  • Name: iqbal-lab-org
  • Login: iqbal-lab-org
  • Kind: organization

Iqbal Lab at EMBL-EBI

GitHub Events

Total
  • Watch event: 1
  • Push event: 2
  • Pull request event: 1
Last Year
  • Watch event: 1
  • Push event: 2
  • Pull request event: 1

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 118
  • Total Committers: 3
  • Avg Commits per committer: 39.333
  • Development Distribution Score (DDS): 0.102
Top Committers
Name Email Commits
Martin Hunt m****t@g****m 106
Michael Hall m****l@m****h 9
martinghunt m****t@u****m 3
Committer Domains (Top 20 + Academic)
mbh.sh: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 15
  • Total pull requests: 30
  • Average time to close issues: 27 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 6
  • Total pull request authors: 3
  • Average comments per issue: 2.4
  • Average comments per pull request: 0.97
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 16 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mbhall88 (7)
  • martinghunt (4)
  • bricoletc (1)
  • Danderson123 (1)
  • jeff-k (1)
  • leoisl (1)
Pull Request Authors
  • martinghunt (24)
  • leoisl (3)
  • mbhall88 (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 5 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 2
pypi.org: varifier

varifier: variant call verification

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 5 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 15.2%
Forks count: 16.8%
Dependent repos count: 21.7%
Average: 24.0%
Downloads: 56.5%
Maintainers (2)
iqbal-lab martinghunt
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • biopython *
  • cluster_vcf_records >=0.13.2
  • mappy >=2.17
  • pandas *
  • pyfastaq >=3.14.0
  • pymummer *
  • pysam *
  • seaborn *
setup.py pypi
  • x.rstrip *
.github/workflows/build.yaml actions
  • actions/checkout v2 composite
  • actions/setup-go v1 composite
  • softprops/action-gh-release v1 composite
Dockerfile docker
  • continuumio/miniconda3 4.9.2 build