agglovar

Agglovar toolkit for fast genomic variant transformations and intersects

Agglovar is a fast toolkit based on Polars to perform fast variant transformations and intersections between callsets. It defines a standard schema for genomic variants based on Apache Arrow, which Polars uses natively. Whenever possible, Aggolvar uses Parquet files to store data allowing it to preserve the schema and take advantage of both columnar storage and pushdown optimizations for fast queries and transformations.

Agglovar replaces variant intersections in the SV-Pop library (https://github.com/EichlerLab/svpop).

The name Agglovar is a portmanteau of the latin word "agglomerare" (to gather) and "variant" (genomic variants).

Alpha release

Agglovar is under active development and a stable release is not yet available.

Documentation

Documentation for Agglovar can be found at: https://agglovar.readthedocs.io/en/latest

Installation

pip install agglovar