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https://github.com/clinical-genomics/varg

variant validation report generator

https://github.com/clinical-genomics/varg

Science Score: 13.0%

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Repository

variant validation report generator

Basic Info
  • Host: GitHub
  • Owner: Clinical-Genomics
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 94.7 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 2
  • Releases: 0
Created over 6 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Changelog Contributing License Codeowners

README.md

Variant Validation Report Generator (VARG)

PyPI version Coverage Status

varg is a simple tool that can be used to benchmark vcf-files against a truth-set of positive controls.

varg simply finds variants between two vcf-files, finds what variants that are common in the two files (with support for imprecise structural variants) and aggregate statistics generated from comparisons between each common variant. The user can dynamically enter what fields and columns that should be compared between the vcf-files. varg supports multi-sample vcf-files.

Installation

varg can be installed with pip

from github: console pip install git+https://github.com/adrosenbaum/varg

from PyPI console pip install varg

or using poetry: poetry install

Usage

To compare two vcf-files, one vcf with positive controls TRUTHVCF, with the vcf to be benchmarked BENCHVCF run the command

console varg compare -t $TRUTH_VCF -v $BENCH_VCF

The samples that are compared between the vcf will default to the respective order of the samples in the vcf-files. The user can specify what samples that should be compared with the -m/--samples-map option e.g. -m child=sample_1,father=sample_2,mother=sample_3 will compare the sample 'child' in the truth-set vcf with sample 'sample_1' in the benchmark-vcf, etc.

To control what fields are compared between the two vcf-files, the user must specify a .py file with the -f/--vcf-fields option. This will default to the file in varg/resources/comparefields. In this file a constant COMPAREFIELDS of python type dict must be declared.

Contributing

Please check out our guide for contributing to demultiplexing

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

GitHub Events

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  • Watch event: 1

Issues and Pull Requests

Last synced: about 1 year ago

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  • Total issues: 0
  • Total pull requests: 15
  • Average time to close issues: N/A
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
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  • Merged pull requests: 0
  • Bot issues: 0
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Top Authors
Issue Authors
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  • adrosenbaum (7)
  • henrikstranneheim (6)
  • dependabot[bot] (1)
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dependencies (1)

Dependencies

poetry.lock pypi
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  • pytest-cov 2.10.1 develop
  • requests 2.25.0 develop
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  • urllib3 1.26.2 develop
  • click 7.1.2
  • coloredlogs 14.0
  • cython 0.29.21
  • cyvcf2 0.10.10
  • humanfriendly 9.0
  • importlib-metadata 3.1.1
  • numpy 1.19.4
  • pyreadline 2.1
  • zipp 3.4.0
pyproject.toml pypi
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  • pytest-cov ^2.10.1 develop
  • Cython ^0.29.21
  • click 7.1.2
  • coloredlogs ^14.0
  • cyvcf2 ^0.10.0
  • importlib-metadata ^3.1.1
  • python ^3.7
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