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

hail

Cloud-native genomic dataframes and batch computing

vcfpy

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

snps

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

fuc

Frequently used commands in bioinformatics

helical

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

truvari

Structural variant toolkit for VCFs

vafator

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

mehari

Python bindings for the mehari variant annotator

granite-suite

A collection of software to work with genomic variants

cutevariant

GUI to visualize and process variant data

vembrane

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

vcfstats

Powerful statistics for VCF files

varfish-cli

Command line interface client for VarFish Server.

svforge

Synthetic VCF generator for structural variants (Manta, DELLY) with controlled variability and realistic artefact injection

haplodynamics

A python library to develop genomic data simulators

igdtools

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

hmtnote

Human mitochondrial variants annotation using HmtVar.

pypgatk

Python tools for proteogenomics

variant-spark

machine learning for genomic variants

tp53

Tools for programmatically annotating VCFs with the Seshat TP53 database

gnomad-db

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

j11hail

Cloud-native genomic dataframes and batch computing