cyvcf2

VCF parser based on htslib (Python 3)

Install

All systems
curl cmd.cat/cyvcf2.sh
Debian Debian
apt-get install python3-cyvcf2
Ubuntu
apt-get install python3-cyvcf2
image/svg+xml Kali Linux
apt-get install python3-cyvcf2
Windows (WSL2)
sudo apt-get update sudo apt-get install python3-cyvcf2
Dockerfile
dockerfile.run/cyvcf2

python3-cyvcf2

VCF parser based on htslib (Python 3)

This modules allows fast parsing of VCF and BCF including region-queries with Python. This is essential for efficient analyses of nucleotide variation with Python on high-throughput sequencing data. cyvcf2 is a cython wrapper around htslib. Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use. This package installs the library for Python 3.