SeqSIMLA2-exact: Simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence

Abstract

Summary: It is difficult for current simulation tools to simulate sequence data in a pre-specified pedigree structure and pre-specified affection status. Previously, we developed a flexible tool, SeqSIMLA2, for simulating sequence data in either unrelated case-control or family samples with different disease and quantitative trait models. Here we extended the tool to efficiently simulate sequences with multiple disease sites in large pedigrees with a given disease status for each pedigree member, assuming that the disease prevalence is low. Availability and implementation: SeqSIMLA2-exact is implemented with C++ and is available at http://seqsimla.sourceforge.net.