snpStats protocols

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snpStats specifications

Information


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

 (6)
2017
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) [, ]. snps in high ld (r2> 0.8 with a snp from the gwas catalogue) were obtained from hapmap3 [], giving a total of 127,594 snps. these were then overlapped with the t-bet binding sites. […]

2016
PMCID: 4862690
PMID: 27163696
DOI: 10.1371/journal.pone.0154998

[…] a multivariate logistic regression analysis was performed to estimate the odds ratio (or) specific for each genotype, with a confidence interval (ci) of 95%, in susceptibility to copd, using the snpstats software []. in order to reduce potential bias generated by the use of multiple tests, we estimate the effective number of independent test in every case where significant differences […]

2016
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 (; ), association testing was done on untransformed data, separately for each study and on each trait. the associations […]

2016
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 [,,] using the snpstats software []. to further define independent predictors of severe bioprosthetic mitral valve calcification, we carried out stepwise logistic regression with the plotting of the roc curve […]

2015
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 (http://cran.r-project.org). we constructed two neighbor-joining trees. one of uncorrected p-distances for individuals using splitstree software [] and one of pairwise fst […]


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snpStats in publications

 (339)
PMCID: 5901134
PMID: 29692628
DOI: 10.2147/CMAR.S154040

[…] hosmer–lemeshow test and the nagelkerke r2 were employed to establish the optimal model. the association between genotypes of the snps and nsclc was analyzed using the inheritance model analysis of snpstats software. five models including the codominant, dominant, recessive, overdominant, and log-additive were analyzed. the best-fit inheritance model was determined using the akaike information […]

PMCID: 5912498
PMID: 29614853
DOI: 10.30773/pi.2017.10.16.1

[…] (spss ver. 18; spss inc., chicago, il, usa)., for the analysis of allele and genotype frequencies, hardy weinberg equilibrium and the association of the drd1 polymorphism with phq-9 scores, the snpstats program was used []. this program employs a linear regression model, which was adjusted for age and gender, in order to find a possible association between the snp in the drd1 gene and phq-9 […]

PMCID: 5885362
PMID: 29618317
DOI: 10.1186/s12864-018-4615-z

[…] d’ > 0.20) associated with two markers, in which case only one of the two markers was removed. we calculated allele frequencies and linkage disequilibrium using the programs genalex 6.501 [] and snpstats []., following doyle et al. [], we quantified error rates associated with snp genotyping using three replicate samples from 9 individuals (27 samples in total). we used genalex 6.501 […]

PMCID: 5892238
PMID: 29769839
DOI: 10.1155/2018/7623823

[…] intervals (95%ci) were calculated as well. finally, multivariate logistic-regression analysis adjusted for gender, age, and apoe-ε4 positivity as possible influencing factors was performed by the snpstats web software available at https://snapstat.net/snpstats/., allele and genotype frequencies of the itga4 −269c/a gene polymorphism (rs113276800) observed in ad patients and control group […]

PMCID: 5869923
PMID: 29616193
DOI: 10.3389/fcimb.2018.00065

[…] of cases and controls. this statistical analysis was performed using medcalc software v 9.3.9.0 (https://www.medcalc.org/). inheritance models and hardy-weinberg equilibrium were assessed by snpstats (https://www.snpstats.net/snpstats/start.htm), a tool based on binary logistic regression analysis (solé et al., ). the choice of best inheritance model for each snp was made by selecting […]


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

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