Tool to Identify individuals with inherited disease-causing variants using SNP chip data.
Please contact the author, Erandee Robertson [email protected], if you would like to report any issues, feedback or feature requests.
If you use FoundHaplo, please acknowledge by citing "Erandee Robertson, Mark F Bennett and Melanie Bahlo. FoundHaplo: Tool to Identify individuals with inherited disease-causing variants using SNP chip data 
Individuals who inherit the same genetic mutation from a common ancestor also share genomic regions on either side of the shared disease-causing variant. This suggests that the presence of a disease-causing genetic variant can be inferred by assessing identity by descent sharing of the variant-associated haplotype between an individual known to have the disease-causing mutation and a patient with unknown aetiology.
Using a Hidden Markov Model, FoundHaplo calculates the FH score, which is the likelihood of identity by descent between the samples of interest and a known disease-causing haplotype and evaluates the resulted scores against a control cohort to predict individuals that carry disease-causing haplotypes using SNP chip data.
see documentation about input file formats and guide to use parallel processing.
devtools::install_github("bahlolab/FoundHaplo")
library(FoundHaplo)git clone --depth=1 https://github.com/bahlolab/FoundHaplo.git