Tag: Sharing

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.

RVsharing 1.7.0 – Computes Estimates of the Probability of Related Individuals Sharing a Rare Variant

RVsharing 1.7.0

:: DESCRIPTION

RVsharing computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them.

::DEVELOPER

Alexandre Bureau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R

:: DOWNLOAD

 RVsharing

:: MORE INFORMATION

Citation

Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
Bureau A, Younkin SG, Parker MM, Bailey-Wilson JE, Marazita ML, Murray JC, Mangold E, Albacha-Hejazi H, Beaty TH, Ruczinski I.
Bioinformatics. 2014 Apr 16. pii: btu198.

MHC v2 – Excess Allele Matching/Sharing in Extended Pedigrees

MHC  v2

:: DESCRIPTION

“MHC“: Matching-Hellinger Distance-Case-Control Quasi Likelihood Tests

::DEVELOPER

The Devlin lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 MHC

:: MORE INFORMATION

Citation:

Lambertus Klei and Kathryn Roeder.
Testing for Association Based on Excess Allele Sharing in a Sample of Related Cases and Controls
Hum Genet. 121: 549-557.

SharedHap 20150114 – Haplotype-sharing Visualization

SharedHap 20150114

:: DESCRIPTION

SharedHap computes and visualize Haplotype-Sharing Patterns among subjects of interests in a pedigree.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C
  • R

:: DOWNLOAD

 SharedHap

:: MORE INFORMATION

Citation:

Hum Hered. 2014;78(1):1-8. doi: 10.1159/000358171.
Visualization of haplotype sharing patterns in pedigree samples.
Kim S1, Saad M, Tsuang DW, Wijsman EM.

BiGG Models 1.6 – A Platform for integrating, standardizing and sharing Genome-scale Models

BiGG Models 1.6

:: DESCRIPTION

BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.

::DEVELOPER

the Systems Biology Research Group at theUniversity of California, San Diego.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

  BiGG Models

:: MORE INFORMATION

Citation:

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.
Nucleic Acids Res. 2015 Oct 17. pii: gkv1049.

Haploclusters – Detect Excess Haplotypes Sharing

Haploclusters

:: DESCRIPTION

HAPLOCLUSTERS is a program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. This LD is often referred to as background LD.

::DEVELOPER

Melanie Bahlo (bahlo@wehi.edu.au) @ WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Haploclusters

:: MORE INFORMATION

Citation:

Bahlo M, Stankovich J, Speed TP, Rubio JP, Burfoot RK, Foote SJ.
Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data.
Hum Genet. 2006 Mar;119(1-2):38-50.

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