SNPTEST pipeline

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

 (41)
2018
PMCID: 5943470
PMID: 29608257
DOI: 10.1002/cam4.1445

[…] software 35 and the 1000 genomes project (2012 release) as the reference panel 9. imputation quality scores ranged from 0.34 to 1.00. association testing on the icogs snps was performed using snptest (v2) 36 employing frequentist tests with a logistic regression model adjusting for eight separate strata and the first 10 principal components 9, 28. these results were then included […]

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 impute23536. 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 […]

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

[…] both german and italian genotypes were imputed into the 1,000 genomes data set (march 2012 haplotypes) using impute2 (ref. 68). association analyses on the imputed data were performed with snptest v2.5.2 (ref. 69)., 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 […]

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

[…] principal components of genetic stratification in japanese as previously described2264 was used to determine the per-allele, additive effect of the snps with a score-based, frequentist algorithm in snptest2. by adding the dosages of rs3825942 and rs1048661 as additional covariates, we tested for independence of our 14 associated snps from the two snps (rs3825942 and rs1048661) of the original […]

2017
PMCID: 5591021
PMID: 28886342
DOI: 10.1016/j.ajhg.2017.08.006

[…] pipeline.20 imputed data were subjected to quality control. we removed snps with info score < 0.3, maf < 1%, or significant deviation from hardy weinberg equilibrium (p < 1 × 106). we used snptest v2.5.221 to calculate the bayes factor for each snp with the assumption that there was only one causal snp per associated region, and the additive model of prior distribution. for regions […]

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

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