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LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces
Author(s) -
Ytournel F.,
Teyssèdre S.,
Roldan D.,
Erbe M.,
Simianer H.,
Boichard D.,
Gilbert H.,
Druet T.,
Legarra A.
Publication year - 2012
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/j.1439-0388.2011.00986.x
Subject(s) - epistasis , pedigree chart , identity by descent , linkage disequilibrium , population , linkage (software) , computer science , evolutionary biology , biology , genetics , haplotype , demography , sociology , gene , genotype
Summary Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re‐create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program ( ldso ) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long‐range LD, allowing optimization of fine‐mapping strategies.