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

variant validation report generator
https://github.com/clinical-genomics/varg

Last synced: 6 days ago
JSON representation

variant validation report generator

• Host: GitHub
• URL: https://github.com/clinical-genomics/varg
• Owner: Clinical-Genomics
• License: mit
• Created: 2019-10-07T11:53:54.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2023-07-25T17:46:16.000Z (over 1 year ago)
• Last Synced: 2023-08-03T21:47:45.475Z (over 1 year ago)
• Language: Python
• Size: 94.7 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

README

        
# Variant Validation Report Generator (VARG)

[![PyPI version](https://badge.fury.io/py/varg.svg)](https://badge.fury.io/py/varg)

[![Coverage Status](https://coveralls.io/repos/github/adrosenbaum/varg/badge.svg?branch=master)](https://coveralls.io/github/adrosenbaum/varg?branch=master)

*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 TRUTH_VCF, with the vcf to be benchmarked BENCH_VCF 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/compare_fields. In this file a constant COMPARE_FIELDS of python type dict must be declared.

## Contributing

Please check out our [guide for contributing to demultiplexing](CONTRIBUTING.md)