IBDseq – Detect IBD Segments using Allele Frequencies

IBDseq

:: DESCRIPTION

IBDseq is a software program for detecting segments of identity-by-descent (IBD) and homozygosity-by-descent (HBD) in unphased genetic sequence data.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

IBDseq

:: MORE INFORMATION

Citation:

Browning BL, Browning SR.
Detecting identity by descent and estimating genotype error rates in sequence data.
Am J Hum Genet. 2013 Nov 7;93(5):840-51. doi: 10.1016/j.ajhg.2013.09.014. Epub 2013 Oct 24. PMID: 24207118; PMCID: PMC3824133.

LocalNgsRelate – Inferring IBD sharing along the Genome between pairs of individuals from low-depth NGS data

LocalNgsRelate

:: DESCRIPTION

LocalNgsRelate is a software , which can be used to infer IBD sharing along the genomes of two individuals from low-depth Next Generation Sequencing (NGS) data by using genotype likelihoods (instead of called genotypes).

::DEVELOPER

LocalNgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LocalNgsRelate

:: MORE INFORMATION

Citation

Severson AL, Korneliussen TS, Moltke I.
LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.
Bioinformatics. 2021 Oct 28:btab732. doi: 10.1093/bioinformatics/btab732. Epub ahead of print. PMID: 34718411.

PEDIBD – Pedigree IBD & Haplotype Inference

PEDIBD

:: DESCRIPTION

PEDIBD infers pairwise Infer identical-by-descent (IBD) and skips haplotype and inheritance construction

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

  PEDIBD

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1411-21. doi: 10.1089/cmb.2011.0167. Epub 2011 Sep 16.
Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference.
Li X1, Li J.

Parente 2.0.1 – Infer Relatedness (IBD) between pairs of Related Individuals

Parente 2.0.1

:: DESCRIPTION

Parente is a method for detecting relatedness. It detects IBD accurately and rapidly using an embedded likelihood ratio test.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Parente

:: MORE INFORMATION

Citation

An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embeddeded Likelihood-Ratio Test.
Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici.
Research in Computational Molecular Biology , Lecture Notes in Computer Science Volume 7821, 2013, pp 212-229

GraphIBD 0.1.0 – Fast IBD Association Testing given Genome-wide SNP data

GraphIBD 0.1.0

:: DESCRIPTION

GraphIBD is a free, open-source IBD association testing software for genome-wide association study analysis. GraphIBD requires an IBD detection method such as Beagle FastIBD to run first. Then GraphIBD builds upon the IBD information to test if the IBD segments show association to the traits.

::DEVELOPER

Buhm Han

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 GraphIBD

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 13.
Fast pairwise IBD association testing in genome-wide association studies.
Han B, Kang EY, Raychaudhuri S, de Bakker PI, Eskin E.

HapFABIA 1.28.0 – Identification of very short Segments of IBD Characterized by Rare Variants

HapFABIA 1.28.0

:: DESCRIPTION

HapFABIA (Factor Analysis for Bicluster Acquisition) is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 HapFABIA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Dec;41(22):e202. doi: 10.1093/nar/gkt1013. Epub 2013 Oct 29.
HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data.
Hochreiter S

RaPID 1.7 – Random Projection-based IBD Detection

RaPID 1.7

:: DESCRIPTION

RaPID is a software of ultra-fast identity by descent (IBD) detection in large cohorts using positional Burrows-Wheeler transform

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

RaPID

:: MORE INFORMATION

Citation

RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts.
Naseri A, Liu X, Tang K, Zhang S, Zhi D.
Genome Biol. 2019 Jul 25;20(1):143. doi: 10.1186/s13059-019-1754-8.

GERMLINE 1.5.1 – Discovery Long Shared Segments of Identity by Descent (IBD) in large populations

GERMLINE 1.5.1

:: DESCRIPTION

GERMLINE is a program for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.

::DEVELOPER

Sasha Gusev 

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 GERMLINE

:: MORE INFORMATION

Citation

Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe’er I (2008)
Whole population, genomewide mapping of hidden relatedness.
Genome Research.2009 Feb;19(2):318-26.