hapFabia

HapFABIA is a computational method to detect very short Identity by Descent (IBD) segments, indicative of shared ancestry, using rare variants found in genomic data. This tool addresses a significant gap in genetic research, where current IBD detection methods primarily focus on long IBD segments found in related individuals and often overlook short IBD segments common among unrelated individuals. The advent of new sequencing technologies has made it possible to identify these short segments through rare variants, offering a high-resolution insight into genetic structures and evolutionary history and improving various genetic analysis techniques like imputation, phasing, and association studies.

Topic

Mapping;Genotype and phenotype

Detail

  • Operation: Haplotype mapping

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.44.0

  • Credit: European Union by an Industry-Academia Partnerships and Pathways (IAPP) project within the 7th framework program.

  • Input: Sequence variations [VCF]

  • Output: Report [TSV] [Textual format] [Image format] [PDF], Nucleic acid features [TSV] [Textual format] [Image format] [PDF], Plot [TSV] [Textual format] [Image format] [PDF], Haplotype map [TSV] [Textual format] [Image format] [PDF]

  • Contact: Andreas Mitterecker mitterecker@bioinf.jku.@

  • Collection: -

  • Maturity: Stable

Publications

  • HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data.
  • Hochreiter S. HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data. HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data. 2013; 41:e202. doi: 10.1093/nar/gkt1013
  • https://doi.org/10.1093/nar/gkt1013
  • PMID: 24174545
  • PMC: PMC3905877

Download and documentation

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