hap-ibd – Detect Identity-by-descent Segments

hap-ibd

:: DESCRIPTION

The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.

::DEVELOPER

Brian L. Browning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

hap-ibd

:: MORE INFORMATION

Citation:

Zhou Y, Browning SR, Browning BL.
A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.
Am J Hum Genet. 2020 Apr 2;106(4):426-437. doi: 10.1016/j.ajhg.2020.02.010. Epub 2020 Mar 12. PMID: 32169169; PMCID: PMC7118582.

CHROMIBD 1.1 – Estimation of Identity-by-Descent Probabilities between Haplotypes and Genotyped Ancestors

CHROMIBD 1.1

:: DESCRIPTION

CHROMIBD computes IBD probabilities between a “target chromosome” and a set of “parental chromosomes” (the method works best without “phantom parental chromosomes”). These chromosomes need to be phased and the program relies only on phased (non-missing) markers in target and parental chromosomes. The program works only with bi-allelic markers such as SNPs.

::DEVELOPER

Unit of Animal Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CHROMIBD

:: MORE INFORMATION

Citation

T. Druet and F. Farnir (2011)
Modeling of identity-bydescent processes along a chromosome between haplotypes and their genotyped ancestors.
Genetics. 2011 June; 188(2): 409–419.

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.