- recipe vcf-pg-loader
High-performance VCF to PostgreSQL loader with clinical-grade compliance
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
vcf-pg-loader is a command-line tool for efficiently loading VCF variant data into PostgreSQL databases. It features streaming VCF parsing with cyvcf2, variant normalization using the vt algorithm, proper Number=A/R/G field handling during multi-allelic decomposition, and binary COPY protocol via asyncpg for maximum insert performance.
- package vcf-pg-loader¶
- versions:
0.5.4-0,0.5.3-0,0.5.1-0- depends anyio:
>=4.3.0- depends asyncpg:
>=0.29.0- depends cyvcf2:
>=0.31.0- depends docker-py:
>=7.0.0- depends pydantic:
>=2.6.0- depends python:
>=3.9- depends rich:
>=13.7.0- depends typer:
>=0.12.0- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install vcf-pg-loader and update with:: mamba update vcf-pg-loader
To create a new environment, run:
mamba create --name myenvname vcf-pg-loader
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/vcf-pg-loader:<tag> (see `vcf-pg-loader/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/vcf-pg-loader/README.html)
