Tag: Relatedness

Coancestry 1.0.1.2 – Simulate, Estimate and Analyse Relatedness and Inbreeding Coefficients

Coancestry 1.0.1.2

:: DESCRIPTION

COANCESTRY is a computer program that implements 7 methods to estimate the pairwise relatedness between individuals and 4 methods to estimate individual inbreeding coefficients, using individual genotypes at a set of marker loci.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

Coancestry

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Coancestry

:: MORE INFORMATION

Citation

COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients.
Wang J.
Mol Ecol Resour. 2011 Jan;11(1):141-5. doi: 10.1111/j.1755-0998.2010.02885.x.

RelateAdmix 0.14 / Relate 0.9992 – Estimating Relatedness between Admixed Individuals

RelateAdmix 0.14 / Relate 0.9992

:: DESCRIPTION

Relate is a method which estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals

RelateAdmix is a software package for inferring relatedness between pairs of individuals even if the individuals are admixed.

::DEVELOPER

RelateAdmix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler / R

:: DOWNLOAD

  RelateAdmix , Relate

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1027-8. doi: 10.1093/bioinformatics/btt652. Epub 2013 Nov 8.
RelateAdmix: a software tool for estimating relatedness between admixed individuals.
Moltke I1, Albrechtsen A.

Anders Albrechtsen, Thorfinn Sand Korneliussen, Ida Moltke, Thomas van Overeem Hansen, Finn Cilius Nielsen, Rasmus Nielsen.
Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium.
Genet Epidemiol. 2009 Apr;33(3):266-74

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

NgsRelate v2.0 – Estimating Pairwise Relatedness from NGS data

NgsRelate v2.0

:: DESCRIPTION

NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.

::DEVELOPER

NgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NgsRelate

:: MORE INFORMATION

Citation

NgsRelate: a software tool for inferring pairwise relatedness from Next Generation Sequencing data.
Korneliussen TS, Moltke I.
Bioinformatics. 2015 Aug 30. pii: btv509

Somalier v0.2.6 – fast Sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs

somalier v0.2.6

:: DESCRIPTION

somalier extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

somalier

:: MORE INFORMATION

Citation:

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches
Brent S Pedersen, Preeti J Bhetariya, Joe Brown, Gabor Marth, Randy L Jensen, Mary P Bronner, Hunter R Underhill, Aaron R. Quinlan.

ML-Relate 20080422 – Estimating Relatedness or Relationship from Genetic data

ML-Relate 20080422

:: DESCRIPTION

ML-Relate is a computer program that calculates maximum likelihood estimates of relatedness and relationship. ML-Relate is designed for microsatellite data, and can accommodate null alleles. It uses simulation to perform two types of hypothesis tests.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

  ML-Relate

:: MORE INFORMATION

Citation

Kalinowski ST, AP Wagner, ML Taper (2006).
ML-Relate: a computer program for maximum likelihood estimation of relatedness and relationship.
Molecular Ecology Notes 6:576-579.