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

fuc

Frequently used commands in bioinformatics

snps

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

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

igdtools

Tools for converting VCF to IGD files and processing them.

variant-spark

machine learning for genomic variants

vembrane

Filter VCF/BCF files with Python expressions.

varfish-cli

Command line interface client for VarFish Server.

cutevariant

A standalone and free application to explore genetics variations from VCF file

pypgatk

Python tools for proteogenomics analysis toolkit

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.

svforge

🛠️ Reproducible, traceable synthetic SV VCFs for testing what your pipeline does to them. Caller-shaped Manta and DELLY outputs, real gnomAD/ENCODE injection with self-verifying tags. Synthetic data only.

hmtnote

Human mitochondrial variants annotation using HmtVar.

j11hail

Cloud-native genomic dataframes and batch computing

haplodynamics

A python library to develop genomic data simulators

variant-extractor

Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.