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Simulation of Rare Variant Genetic Data

Bioconductor version: Release (3.19)

Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

Author: Megan Null [aut], Ryan Barnard [cre]

Maintainer: Ryan Barnard <rbarnard1107 at>

Citation (from within R, enter citation("RAREsim")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

RAREsim Vignette HTML R Script
Reference Manual PDF


biocViews Genetics, Sequencing, Software, VariantAnnotation
Version 1.8.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.1.0)
Imports nloptr
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Suggests markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package RAREsim_1.8.0.tar.gz
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macOS Binary (x86_64) RAREsim_1.8.0.tgz
macOS Binary (arm64) RAREsim_1.8.0.tgz
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Source Repository (Developer Access) git clone
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