Visual display of homozygous regions in SNP data files
IBDfinder displays a graphical plot that identifies runs of homozygous SNPs within Affymetrix SNP chip data. Such regions often represent chromosomal segments that are identical by descent (IBD), and are possible locations for recessive disease-causing genes.
Data from several SNP chips can be loaded, allowing the generation of a second graph (lower part of panel) that identifies regions of IBD in common between several individuals.
IBDfinder takes a qualitative approach to identification of IBD regions. It ignores linkage disequilibrium and pedigree structure, thereby allowing the analysis of singletons and groups of unrelated individuals.
A fuller description of IBDfinder and the SNPsetter utility for integrating disparate SNP sets:
Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT (2009) IBDfinder and SNPsetter: tools for
pedigree-independent identification of autozygous regions in individuals with recessive inherited disease.
Human Mutation 30: 960-967.
PubMed | Manuscript | Published version
A detailed “walk-through” explanation, with screenshots, of how to use IBDfinder:
HTML guide (single large page)
If you are using Affymetrix SNP5 or SNP6 genotype data, or data extracted by the Genotyping Console version 2 or above, the files must be annotated using SNPannotator.
The download page has instructions on system requirements and installation of IBDfinder
If you need to use IBDfinder with Illumina SNP data, you may want to look here first.