XIBD: software for inferring pairwise identity by descent on the X chromosome

Lyndal Henden; David Wakeham; Melanie Bahlo

doi:10.1093/bioinformatics/btw124

XIBD: software for inferring pairwise identity by descent on the X chromosome

Bioinformatics. 2016 Aug 1;32(15):2389-91. doi: 10.1093/bioinformatics/btw124. Epub 2016 Mar 21.

Authors

Lyndal Henden¹, David Wakeham², Melanie Bahlo³

Affiliations

¹ Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia Department of Medical Biology.
² School of Physics.
³ Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia Department of Medical Biology School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia.

PMID: 27153693
DOI: 10.1093/bioinformatics/btw124

Abstract

XIBD performs pairwise relatedness mapping on the X chromosome using dense single nucleotide polymorphism (SNP) data from either SNP chips or next generation sequencing data. It correctly accounts for the difference in chromosomal numbers between males and females and estimates global relatedness as well as regions of the genome that are identical by descent (IBD). XIBD also generates novel graphical summaries of all pairwise IBD tracts for a cohort making it very useful for disease locus mapping.

Availability and implementation: XIBD is written in R/Rcpp and executed from shell scripts that are freely available from http://bioinf.wehi.edu.au/software/XIBD along with accompanying reference datasets.

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Chromosomes, Human, X*
Female
Genome-Wide Association Study
High-Throughput Nucleotide Sequencing*
Humans
Male
Polymorphism, Single Nucleotide
Software*