Variant Analysis Python Packages

bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

biocommons-seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

alphafold-sovereign-mcp

BioMed MCP over AlphaFold DB + 8 public sources, with SQLite knowledge graph, offline mode, and explicit clinical-use limits.

tinyhgvs

Lightweight HGVS variant parser

seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

granite-suite

A collection of software to work with genomic variants

variant-extractor

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

alphagenome-viewer

Web app for interacting with Google DeepMind's AlphaGenome model — interval predictions, variant effect analysis, and visualization

biocommons-anyvar

Lightweight, portable variation registration and retrieval

anyvar

Lightweight, portable variation registration and retrieval

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

graphmana

Graph-native data management platform for variant genomics

mrva

A terminal-first approach to CodeQL multi-repo variant analysis

vstol

Variant Standardization, Tabulation, and Operations Library

embedpvp

EmbedPVP: Embedding-based Phenotype Variant Predictor

varexpm

A CLI-Tool for extracting context-based process variants from conventional event logs.