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

truvari

Structural variant toolkit for VCFs

helical

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

vmware-privateai

VMware Private AI Foundation with NVIDIA ops — GPU inventory, vGPU/DirectPath profiles, utilization, model serving (MCP + CLI). Community, not affiliated with VMware/Broadcom/NVIDIA.

igdtools

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

snputils

Python toolkit for fast genotype I/O, ancestry analysis, population-genetics statistics, genotype QC, GWAS, and visualization

fuc

Frequently used commands in bioinformatics

octopusv

Merge and compare structural variants across callers, samples, and platforms. Standardizes BND-heavy output from GRIDSS, SvABA, Sniffles, and more.

alphavx

CLI tool that batch-scores VCF variants against AlphaGenome and generates interpretable multi-modal effect reports.

vembrane

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

mehari

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

vafator

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

pie-phasing-eval

Phasing all-In-one Evaluator

birthdays-cli

A command-line utility for displaying and managing birthdays from JSON- or vCard-based contacts.

varfish-cli

VarFish REST API client (CLI + Python package)

cutevariant

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

admissible

Audit whether exome data can support an interpretation, before the interpretation.

granite-suite

A collection of software to work with genomic variants

pynnotator

This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.

hmtnote

Human mitochondrial variants annotation using HmtVar.