- recipe bacprune
Fast LD pruning of haploid genotype matrices
- Homepage:
- License:
MIT
- Recipe:
BacPrune-Rust prunes a haploid genotype matrix by linkage disequilibrium (LD) threshold. Three modes are available:
--r Greedy pruning by r² (Pearson r-squared) threshold (default). --dprime Greedy pruning by |D'| threshold. --dedup Hash-based exact-duplicate removal only (O(n·v), no pairwise
LD calculation).
All modes first remove exact duplicate variant columns via hashing before any threshold-based pruning. Output includes the pruned genotype matrix, a pruning summary, and a per-variant correlation-direction file.
- package bacprune¶
- Versions:
0.9.0-0- Additional platforms:
linux-aarch64,osx-arm64
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 bacprune
to add into an existing workspace instead, run:
pixi add bacprune
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 bacprune
Alternatively, to install into a new environment, run:
conda create -n envname bacprune
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/bacprune:<tag>
(see bacprune/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¶
Link to this page¶
Render an 
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