VCFPy

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

• Free software: MIT license
• Documentation: https://vcfpy.readthedocs.io.

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.