gdsfmt statistics

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gdsfmt specifications

Information


Unique identifier OMICS_19564
Name gdsfmt
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 1.12.0
Stability Stable
Source code URL https://codeload.github.com/zhengxwen/gdsfmt/zip/v1.7.17
Maintained Yes

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Documentation


Maintainer


  • person_outline Xiuwen Zheng <>

Additional information


http://zhengxwen.github.io/gdsfmt/release/help/gdsfmt-package.html http://bioconductor.org/packages/release/bioc/html/gdsfmt.html http://corearray.sourceforge.net/tutorials/gdsfmt/

Publication for gdsfmt

gdsfmt in publications

 (5)
PMCID: 5788914
PMID: 29422910
DOI: 10.3389/fpls.2018.00029

[…] (he) were calculated with ‘adegenet’ (; ). the inbreeding coefficient (fis) was calculated following the formula 1 - (ho/he). principal component analysis (pca) was conducted using ‘snprelate’ and ‘gdsfmt’ (). calculations for nei’s distance (dst) () and pairwise fixation index (fst) among populations were performed with 1,000 bootstrap replications using ‘stampp’ (). the analysis of molecular […]

PMCID: 5708779
PMID: 29190814
DOI: 10.1371/journal.pone.0188920

[…] current study) or both alleles were extracted from the rice snp-seek database, and merged with the snps from seeragasamba. the merged vcf was converted into genomic data structure (gds) format using gdsfmt package of r software (https://www.r-project.org/). bi-allelic snps were extracted from the gds file. snprelate program from r package was used to generate dendrogram using identity-by-state […]

PMCID: 5518283
PMID: 28370647
DOI: 10.1111/mec.14123

[…] filtered with vcftools by retaining only snps with the minor allele present in at least two individuals. the retained 129,511 biallelic snps were imported in the bioconductor (huber et al., ) with gdsfmt, and the pca was finally drawn with the r package snprelate (zheng et al., )., synthetic transcripts of each sample have been generated from the gatk‐filtered vcf file with the gatk […]

PMCID: 4797340
PMID: 26988219
DOI: 10.1186/s12864-016-2568-7

[…] neighbor-joining algorithm, and visualized by figtree v1.4.0 []. the snp marker matrix used for pca analysis was obtained from the variant call format (vcf) files generated by tassel v4.3.5, using gdsfmt and snprelate [] packages implemented on the statistical software r []., in order to estimate the number of sub-populations in the sampled plant accessions, a bayesian model clustering […]

PMCID: 4488844
PMID: 26132555
DOI: 10.1371/journal.pone.0130329

[…] shared was over 0.125, and outliers by principal-component analysis (pca) [] () were previously excluded. we estimated the ibd sharing score using plink’s ‘-genome’ option [] and performed pca using gdsfmt and snprelate packages in the statistical software r []. we also excluded all snvs with a genotype call rate < 0.80, a hardy-weinberg equilibrium p-value < 1×10-6 or nongenic […]


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gdsfmt institution(s)
Department of Biostatistics, University of Washington, Seattle, WA, USA
gdsfmt 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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