snpStats pipeline

snpStats specifications


Unique identifier OMICS_02091
Name snpStats
Interface Web user interface
Restrictions to use None
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Publication for snpStats

snpStats IN pipelines

PMCID: 5328407
PMID: 28187197
DOI: 10.1371/journal.pgen.1006587

[…] used in downstream analysis. snps not in hapmap3 were removed, giving 13,936 autosomal snps in the final analysis. data were analysed using the bioconductor snpmatrix programme (recently updated to snpstats) [72, 73]. snps in high ld (r2> 0.8 with a snp from the gwas catalogue) were obtained from hapmap3 [74], giving a total of 127,594 snps. these were then overlapped with the t-bet binding […]

PMCID: 4900668
PMID: 27280446
DOI: 10.1371/journal.pone.0156914

[…] ~4.5 million autosomal snps (r2 > 0.3, maf > 0.001). the data were collated in posterior probabilities from genotype dosage, incorporating imputation uncertainty, to be used by the r package snpstats., based on descriptive statistics and visual inspection (table 1; s1 fig), association testing was done on untransformed data, separately for each study and on each trait. the associations […]

PMCID: 5037665
PMID: 27589735
DOI: 10.3390/ijms17091385

[…] snps. laboratory staff was blinded to patient status, and one-tenth of the samples was repeatedly genotyped for quality control., the statistical analysis was performed as in [22,23,24] using the snpstats software [25]. to further define independent predictors of severe bioprosthetic mitral valve calcification, we carried out stepwise logistic regression with the plotting of the roc curve […]

PMCID: 4471085
PMID: 26083354
DOI: 10.1371/journal.pone.0128688

[…] step of 5 snps, and pairwise r2 threshold of 0.1, resulting in 10,260 independent snp markers. the second snp set was for population analysis., principal component analysis (pca) was conducted using snpstats in r ( we constructed two neighbor-joining trees. one of uncorrected p-distances for individuals using splitstree software [6] and one of pairwise fst […]

PMCID: 4593624
PMID: 26437075
DOI: 10.1371/journal.pone.0139642

[…] assigning the case-control status arbitrarily., the simulations and power assessment where done using the computer program r 3.2.1 [44], with the additional packages: matrix [45], multiphen [46] and snpstats [47]., the simulation program can be received from the authors by request., both of the statistical methods keep the type-i error level, with skat being slightly more conservative than wss. […]

snpStats institution(s)
Catalan Institute of Oncology, IDIBELL, Epidemiology and Cancer Registry L'Hospitalet, Barcelona, Spain

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