Simulation of Chromosomal Regions Shared by Family Members
Conversion of genetic map positions
Custom recombination map
Estimation of one- and two-locus relatedness coefficients
Extract ID labels from simulation output
Find specific IBD patterns
Draw haplotypes onto a pedigree plot
IBD simulation
ibdsim2: Simulation of Chromosomal Regions Shared by Family Members
Diploid karyogram
Karyogram plots
Haploid karyogram
Launch the ibdsim2 app
Load a built-in genetic map
Physical and genetic map lengths
Scatter plots of IBD segment distributions
Simulate markers conditional on a given IBD pattern
Realised relatedness
Summary statistics for identified segments
Uniform recombination maps
Probability of zero IBD
Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Halldorsson et al. (2019) <doi:10.1126/science.aau1043>), phased chromosomes are simulated for all pedigree members. Applications include calculation of realised relatedness coefficients and IBD segment distributions. 'ibdsim2' is part of the 'pedsuite' collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite', including a separate chapter on 'ibdsim2', is available in the book 'Pedigree analysis in R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising and comparing IBD distributions is available at <https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Useful links