https://github.com/bihealth/vcfpy

Python 3 library with good support for both reading and writing VCF
https://github.com/bihealth/vcfpy

bioinformatics file-format parsing vcf writing

Last synced: 5 months ago
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Python 3 library with good support for both reading and writing VCF

• Host: GitHub
• URL: https://github.com/bihealth/vcfpy
• Owner: bihealth
• License: mit
• Created: 2016-09-15T07:59:19.000Z (almost 10 years ago)
• Default Branch: main
• Last Pushed: 2025-10-02T06:37:31.000Z (10 months ago)
• Last Synced: 2026-02-01T12:40:37.747Z (6 months ago)
• Topics: bioinformatics, file-format, parsing, vcf, writing
• Language: Python
• Homepage:
• Size: 1.41 MB
• Stars: 112
• Watchers: 4
• Forks: 24
• Open Issues: 13
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst
  • Codemeta: codemeta.json

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# VCFPy

Python 3 VCF library with good support for both reading and writing

- Free software: MIT license

- Documentation: .

## Features

- Support for reading and writing VCF v4.3

- Interface to `INFO` and `FORMAT` fields is based on `dict` allows for easier modification than PyVCF (also I find this more pythonic)

- Read (and jump in) and write BGZF files just using `vcfpy`

## Why another VCF parser for Python!

I've been using PyVCF with quite some success in the past. However, the

main bottleneck of PyVCF is when you want to modify the per-sample

genotype information. There are some issues in the tracker of PyVCF but

none of them can really be considered solved. I tried several hours to

solve these problems within PyVCF but this never got far or towards a

complete rewrite...

For this reason, VCFPy was born and here it is!

## What's the State?

VCFPy is the result of two full days of development plus some

maintenance work later now (right now). I'm using it in several projects

but it is not as battle-tested as PyVCF.

## Why Python 3 Only?

As I'm only using Python 3 code, I see no advantage in carrying around

support for legacy Python 2 and maintaining it. At a later point when

VCFPy is known to be stable, Python 2 support might be added if someone

contributes a pull request.