RVS statistics

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Associated diseases

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RVS specifications

Information


Unique identifier OMICS_20119
Name RVS
Alternative name Rare Variant Sharing
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3.1
Stability Stable
Requirements
methods, stats, utils, testthat, BiocStyle, rmarkdown, knitr, snpStats, R(>=3.4.0), kinship2, gRain
Maintained Yes

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Maintainers


  • person_outline Thomas Sherman <>
  • person_outline Alexandre Bureau <>

Additional information


Manual: http://bioconductor.org/packages/devel/bioc/manuals/RVS/man/RVS.pdf

Publication for Rare Variant Sharing

RVS in publications

 (3)
PMCID: 4926957
PMID: 27270105
DOI: 10.1038/ng.3583

[…] other long-range phasing methods., in other work, we have shown that large and accurately phased haplotype reference panels can be used to help phase single sequenced samples. this approach uses rare variant sharing between the sequenced sample and the reference panel to efficiently select a set of template haplotypes to use within the hmm model. the oxford statistics phasing server allows […]

PMCID: 4125085
PMID: 25101869
DOI: 10.1371/journal.pgen.1004528

[…] , , may make an important contribution to genetic susceptibility to disease –, and provide information about both demographic history, and fine-scale population structure , . while patterns of rare variant sharing are informative in themselves, knowing the age of the variants allows us to observe changes in structure over time, and thus to infer the dates of demographic events., rare […]

PMCID: 3736321
PMID: 23698362
DOI: 10.1038/nature12170

[…] with known duplicates or relatedness (as distant as first cousins) were excluded, relatedness was later confirmed by immunochip genome wide identity-by-state analysis and by analysis of multiple rare variant sharing in fluidigm sequencing data. additional independent european samples genotyped for rs17849502 (4,313 coeliac cases and 3,954 controls) were previously described., pcr primers […]


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RVS institution(s)
Département de Médecine Sociale et Préventive, Université Laval, QC, Canada; Centre de recherche CERVO, QC, Canada; Office of Biostatistics, Food and Drug Administration, Silver Spring, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Channing Division of Network Medicine, Harvard Medical School, Boston, MA, USA; Prime Health Clinic Jeddah, Riyadh, Saudi Arabia; Institute of Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA; Department of Pediatrics, School of Medicine, University of Iowa, Iowa City, IA, USA; Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Inherited Disease Research Branch, National Human Genome Research Institute, Baltimore, MD, USA
RVS funding source(s)
Supported by NIDCR grant R03-DE-02579.

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