SNPRelate pipeline

SNPRelate specifications

Information


Unique identifier OMICS_19567
Name SNPRelate
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.10.2
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Xiuwen Zheng <>

Additional information


http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html

Publication for SNPRelate

SNPRelate citations

 (3)
2016
PMCID: 4946207

[…] further information on the genetic differentiation within a population and between populations. further, a principal components analysis based on the genetic data (pca) was carried out with the snprelate package in r [35] describing patterns of population differentiation and overlap. clustering of breeds into genetic groups and estimation of breed proportions of ancestral breeds was carried […]

2015
PMCID: 4478540

[…] g. hirsutum chromosome, were also genotyped for the same markers., the vcf file produced from gatk that included genotypes from all 14 samples was imported into r (r development core team 2010). the snprelate package (zheng et al. 2012) was used to perform a principle component analysis, and eigenvalue1 and eigenvalue2 were used to visualize samples. a distance matrix was determined […]

2014
PMCID: 4284805

[…] mcmc scheme under the crossing-over model of interval in ldhat69, with 10 million iterations and 5 million burn-ins. population structure was examined using a principal component analysis in snprelate70. the demographic history of atlantic and mediterranean sea bass populations was inferred from their joint site frequency spectrum (sfs) in δaδi v1.6.3 (ref. 39). we used 109,329 snps […]

SNPRelate institution(s)
Department of Biostatistics, University of Washington, Seattle, WA, USA
SNPRelate funding source(s)
Supported by US National Institutes of Health, Genes, Environment and Health Initiative. Genetics Coordinating Center (U01 HG 004446).

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