SNPRelate protocols

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description
SNPRelate computational protocol

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 IN pipelines

 (4)
2017
PMCID: 5637501
PMID: 29025941
DOI: 10.1128/genomeA.01066-17

[…] the reads to the k10 m. avium subsp. paratuberculosis reference genome (14) using bwa-mem (16) and calling variation with gatk haplotype caller (17). this resulted in a dendrogram, built with snprelate (18), with three clearly differentiated groups for the type c, type s pigmented, and type s nonpigmented strains. the pigmented m. avium subsp. paratuberculosis isolate was unequivocally […]

2016
PMCID: 4946207
PMID: 27418004
DOI: 10.1186/s12863-016-0416-z

[…] 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 […]

2016
PMCID: 5111214
PMID: 27846816
DOI: 10.1186/s12863-016-0455-5

[…] visualise and explore the correlation between significant snps, obtained in the several association analyses, and colour phenotypes, a principal component analysis (pca) was done using r package snprelate (bioconductor v3.2; r v3.2.3) implemented in the vcf2pca.r script [59]., to attempt potential de novo assembly of the genome, genomic dna of one p. spumarius individual from quinta do bom […]

2014
PMCID: 4284805
PMID: 25534655
DOI: 10.1038/ncomms6770

[…] 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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