Simulates whole autosomes from real genomic segments in a way that preserves the input autosomes' linkage disequilibrium (LD) pattern. Long Description (required) REGENS (REcombinatory Genome ENumeration of Subpopulations) is an open-source Python package that simulates whole genomes from real genomic segments. REGENS recombines these segments in a way that simulates completely new individuals while simultaneously preserving the input genomes' linkage disequilibrium (LD) pattern with extremely high fidelity. It takes plink (bed, bim, fam) file sets of existing genotype data as input and produces new (bed, bim, fam) file sets as output. REGENS can also simulate mono-allelic and epistatic single nucleotide variant (SNV) effects on a continuous or binary phenotype without perturbing the simulated LD pattern. REGENS was measured to be 88.5 times faster and require 6.2 times lower peak RAM on average than a similar algorithm called Triadsim.
Our publication (https://doi.org/10.21105/joss.02743) and supplementary repository (https://github.com/EpistasisLab/regens-analysis) both contain more technical details.
See our REGENS repository (REGENS repository (https://github.com/EpistasisLab/regens) for the source code, as well as detailed instructions and examples. gwas-tools, simulated-datasets https://github.com/EpistasisLab/regens/tags firstname.lastname@example.org Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator. Every sub-attribute is selected Not all sub-attributes are selected Fill Clear Expand Collapse Reset Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s). Can't Find the Attribute You Are Looking For?
If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the
Additional Comment box of the Submit tab. Summary of Proposed Changes Current Citations/Applications ,
REGENS: an open source Python package for simulating realistic autosomal genotypes JOSS,
https://joss.theoj.org/papers/10.21105/joss.02743, Primary Citation