SNPTEST protocols

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SNPTEST specifications

Information


Unique identifier OMICS_04400
Name SNPTEST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.5.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jonathan Marchini <>

Publication for SNPTEST

SNPTEST in pipelines

 (51)
2018
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] in the german data set, eigenvectors were inferred using the “smartpca” component within eigensoft v2.4 and adjustment was carried out by including the first two eigenvectors as covariates in snptest during association analysis,. the inflation factor λ and λ1000 was again calculated for all snps post imputation, qc,. the association between each snp and risk was calculated using snptest […]

2018
PMCID: 5940112
PMID: 29695640
DOI: 10.18632/aging.101423

[…] by comparing cases with and without a certainly given subphenotype., linkage disequilibrium (ld) patterns were analyzed and displayed by haploview []. logistic regression tests were performed using snptest v2.5b []. tests of independent contributions toward disease associations for snps in a single locus were done using logistic regression, adjusting for the effect of a specific snp […]

2017
PMCID: 5341021
PMID: 28272517
DOI: 10.1038/srep44114

[…] (build 37/hg19) on chromosome 17. association analysis was performed for males-only, females-only and combined male and female samples of hypertensive patients versus normotensive controls using snptest, the companion program to impute2. a logistic regression model with additive genotype coding and with pc1, pc2, age, body mass index (bmi), and genotyping batch and genotyping array (5.0 vs. […]

2017
PMCID: 5414179
PMID: 28447668
DOI: 10.1038/ncomms15034

[…] before the association analysis. association analysis between snps and case control status were performed using the score test of the log additive genetic effect with covariate adjustment using snptest as previously described. imputation and association analysis for melanoma was performed using 1000g (phase 1 integrated release 3, march 2012) as previously described. imputation for lung […]

2017
PMCID: 5457519
PMID: 28534485
DOI: 10.1038/ncomms15466

[…] previously. both german and italian genotypes were imputed into the 1,000 genomes data set (march 2012 haplotypes) using impute2 (ref. ). association analyses on the imputed data were performed with snptest v2.5.2 (ref. )., a logistic regression model using gender and age as covariates in german and italian samples and the first six principal components of genetic stratification in japanese […]


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SNPTEST in publications

 (328)
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z

[…] for the tcga pan-glioma analysis, and classification schemes were adopted from eckel-passow, et al. and ceccarelli, et al.., the data were analyzed using sex-stratified logistic regression models in snptest for all snps on autosomal chromosomes within 500 kb of previously identified risk loci, and/or those found to be nominally significant (p < 5 × 10−4) in a previous meta-analysis (fig. ),. […]

PMCID: 5934841
PMID: 29724251
DOI: 10.1186/s13075-018-1590-3

[…] x chromosome data. in all the studies, snps with an imputation score < 0.9 were removed from further analysis., the x chromosomal snps passing quality control were analyzed for association using snptest [], fitting a logistic regression model in males and females separately. the association for european data, which comprise samples derived from different cohorts [], was adjusted using four […]

PMCID: 5940112
PMID: 29695640
DOI: 10.18632/aging.101423

[…] by comparing cases with and without a certainly given subphenotype., linkage disequilibrium (ld) patterns were analyzed and displayed by haploview []. logistic regression tests were performed using snptest v2.5b []. tests of independent contributions toward disease associations for snps in a single locus were done using logistic regression, adjusting for the effect of a specific snp […]

PMCID: 5892035
PMID: 29631575
DOI: 10.1186/s12931-018-0762-7

[…] into normally distributed z scores using the r function ‘rntransform’ [] (additional file : figure s1). we performed gwas for three transformed phenotypes: eco, salivary cotinine and cpd using snptest [] assuming an additive genetic model and adjusting for age, gender, and the first 5 genetic principal components (pcs). since cotinine levels were measured in all subjects at baseline visit, […]

PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] table ). conditional analysis did not provide evidence for multiple independent signals at either 8q24.21 or 2q22.3.fig. 1fig. 2table 1note: p-values for each individual study were generated using snptest v2.5.2 software. combined p-values and estimates were obtained using a fixed-effects model using beta values and standard errors. raf risk allele frequency, or odds ratio, phet p […]


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SNPTEST institution(s)
Department of Statistics, University of Oxford, Oxford, UK

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