Vcf Python Packages

vobject

A full-featured Python package for parsing and creating iCalendar and vCard files

cyvcf2

cython + htslib == fast VCF and BCF processing

vcfpy

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

hail

Cloud-native genomic dataframes and batch computing

snps

tools for reading, writing, generating, merging, and remapping SNPs

fuc

Frequently used commands in bioinformatics

truvari

Structural variant toolkit for VCFs

mehari

VEP-like tool for sequence ontology and HGVS annotation of VCF files

helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

vcf-super-cli

Modern, agent-friendly CLI for VMware Cloud Foundation 9 (vSphere + NSX), with a command tree generated dynamically from the vcf-sdk vAPI bindings.

vafator

Annotate variants in a VCF file with technical annotations from one or more BAMs

igdtools

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

vembrane

vembrane filters, sorts, and transforms VCF records using python expressions

htslurp

slurp noodles-htsget streams into python

rubam

Pure-Rust BAM/CRAM depth, pileup and stats — fast, multi-threaded, Windows-native. Originally forked from rustbam.

cutevariant

GUI to visualize and process variant data

granite-suite

A collection of software to work with genomic variants

varfish-cli

Command line interface client for VarFish Server.

bioartifact

Lightweight, agent-friendly inspection and contract validation for bioinformatics artifacts.

hmtnote

Human mitochondrial variants annotation using HmtVar.

vcfstats

Powerful statistics for VCF files

gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

haplodynamics

A python library to develop genomic data simulators

pypgatk

Python tools for proteogenomics analysis toolkit