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/).

tinyhgvs

Hybrid Rust/Python library for parsing HGVS variants.

granite-suite

A collection of software to work with genomic variants

seqrepo

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

gnomad-db

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

variant-extractor

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

graphmana

Graph-native data management platform for variant genomics

alphagenome-viewer

Web interface for Google DeepMind's AlphaGenome genomic prediction model

biocommons-anyvar

Lightweight, portable variation registration and retrieval

anyvar

AnyVar provides Python and REST interfaces to validate, normalize, generate identifiers, and register biological sequence variation according to the GA4GH Variation Representation standards.

embedpvp

EmbedPVP: Embedding-based Phenotype Variant Predictor

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

mrva

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

vstol

Variant Standardization, Tabulation, and Operations Library

varexpm

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