recipe basevar

High-performance variant caller for ultra-low-depth WGS and NIPT data

Homepage:

https://github.com/ShujiaHuang/BaseVar2

Documentation:

https://github.com/ShujiaHuang/BaseVar2#readme

License:

AGPL / AGPL-3.0-or-later

Recipe:

/basevar/meta.yaml

Links:

doi: 10.1016/j.xgen.2024.100669

BaseVar is a fast, memory-efficient C++17 variant caller for ultra-low-depth (<1x) sequencing data, designed for non-invasive prenatal testing (NIPT) and population-scale genomics. It simultaneously identifies genomic variants and estimates allele frequencies in cohorts of tens to hundreds of thousands of samples.

Key features: - Designed for ultra-low-depth (<1x) WGS data - Supports NIPT (non-invasive prenatal testing) mixed genome scenarios - Simultaneous variant calling and allele frequency estimation - Handles cohorts of tens to hundreds of thousands of samples - Over 100x faster than the original Python implementation - 5-10x faster than BaseVar v1 - Typically requires only 3-4 GB RAM with -B 200

Originally introduced in a Cell paper (2018), with a completely redesigned C++17 implementation described and benchmarked in Cell Genomics (2024).

package basevar

(downloads) docker_basevar

Versions:

2.6.7-0

Depends:

  • on __glibc >=2.17,<3.0.a0

  • on bzip2 >=1.0.8,<2.0a0

  • on htslib >=1.18

  • on htslib >=1.24,<1.25.0a0

  • on libcurl >=8.21.0,<9.0a0

  • on libgcc >=14

  • on liblzma >=5.8.3,<6.0a0

  • on libstdcxx >=14

  • on libzlib >=1.3.2,<2.0a0

  • on openssl >=3.5.7,<4.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install basevar

to add into an existing workspace instead, run:

pixi add basevar

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install basevar

Alternatively, to install into a new environment, run:

conda create -n envname basevar

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/basevar:<tag>

(see basevar/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/basevar/README.html)