Registration Open for Bioc2024 July 24-26


hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Bioconductor version: Release (3.19)

A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

Author: Sepp Hochreiter <hochreit at>

Maintainer: Andreas Mitterecker <mitterecker at>

Citation (from within R, enter citation("hapFabia")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

hapFabia: Manual for the R package PDF R Script
Reference Manual PDF


biocViews Clustering, GeneticVariability, Genetics, SNP, SequenceMatching, Sequencing, Software, Visualization
Version 1.46.0
In Bioconductor since BioC 2.11 (R-2.15) (12 years)
License LGPL (>= 2.1)
Depends R (>= 3.6.0), Biobase, fabia(>= 2.3.1)
Imports methods, graphics, grDevices, stats, utils
System Requirements
See More
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package hapFabia_1.46.0.tar.gz
Windows Binary
macOS Binary (x86_64) hapFabia_1.46.0.tgz
macOS Binary (arm64) hapFabia_1.46.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats