XIBD

XIBD performs pairwise relatedness mapping on the X chromosome using dense single nucleotide polymorphism (SNP) data to identify identical-by-descent (IBD) regions and estimate relatedness for studies of X-linked inheritance.

Key Features:

• X chromosome pairwise mapping: Performs pairwise relatedness mapping specifically on the X chromosome using dense SNP data.
• Input data types: Accepts SNP chip and next-generation sequencing (NGS) data.
• Sex-specific handling: Accounts for differences in chromosomal numbers between males and females to ensure accurate relatedness estimation.
• Global and local relatedness: Estimates global relatedness and identifies specific genomic regions that are identical by descent (IBD).
• Graphical summaries: Generates graphical summaries of all pairwise IBD tracts for a cohort.
• Implementation: Implemented in R and Rcpp and executed via shell scripts.
• Reference datasets: Provides accompanying reference datasets.

Scientific Applications:

• Genetic linkage and disease locus mapping: Supports mapping of loci involved in X-linked diseases by identifying shared IBD regions.
• Studies of heritability and X-linked traits: Facilitates investigation of inheritance patterns and heritability for X-linked phenotypes.
• Cohort-level ancestry and relatedness analysis: Enables cohort-wide identification and visualization of pairwise IBD tracts to detect shared ancestry.

Methodology:

Performs pairwise relatedness mapping on the X chromosome using dense SNP data from SNP chips or next-generation sequencing, accounts for sex-specific chromosome counts, estimates global relatedness and identifies IBD tracts, and produces graphical summaries; implemented in R/Rcpp and run via shell scripts.