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SNPMStat specifications


Unique identifier OMICS_08985
Name SNPMStat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes


No version available

Publications for SNPMStat

SNPMStat citations


A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants

PLoS One
PMCID: 4074155
PMID: 24972110
DOI: 10.1371/journal.pone.0101025

[…] nt (IBD), among individuals . Imputation methods have been developed to use either of them, or both with different degrees of complexity. These methods include allele frequencies based methods(PLINK, SNPMSTAT, UNPHASED, and TUNA), Hidden Markov Chain based methods(IMPUT, MACH, fastPHASE), mixed model based methods (S-MM,M-MM) and graphic theory based method(BEAGLE) –. A clear linkage phase, such a […]


Simpute: An Efficient Solution for Dense Genotypic Data

Biomed Res Int
PMCID: 3581137
PMID: 23509783
DOI: 10.1155/2013/813912

[…] We used samples from HapMap Phase II release 22 as the reference data set, which is required by BEAGLE, BIMBAM, MACH, SNPMStat, IMPUTE, and plink. Because of the intractable computation load of SNPMStat and IMPUTE, we divided the chromosome into segment of 10,000 SNPs for the inputs. Because SNPMStat requires substan […]


A Fine Mapping Study of 7 Top Scoring Genes from a GWAS for Major Depressive Disorder

PLoS One
PMCID: 3359349
PMID: 22649524
DOI: 10.1371/journal.pone.0037384

[…] was used for imputing 2037829 autosomal SNPs with r2≥0.5 (which removes approximately 90% of SNPs with unreliable imputation results, while dropping only 2–3% of reliably imputed SNPs) and using the SNPMStat method , 246 SNPs in the PCLO area were imputed. The HapMap2 CEU panel was used as a reference .In this study, imputation was only performed for missing genotypes, rather than for all new tag […]


Analyses and Comparison of Imputation Based Association Methods

PLoS One
PMCID: 2877082
PMID: 20520814
DOI: 10.1371/journal.pone.0010827
call_split See protocol

[…] Seven popular imputation-based association methods were investigated in this study: MACH2qtl/dat, SNPTEST, ProbABEL, Beagle, Plink, BIMBAM and SNPMStat. To control imputation quality, the respective quality-control (QC) cut-off recommended by each method was used. In cases where no cut-off was available, an empirical setting from extensive r […]


Genomewide Association for Major Depressive Disorder: A possible role for the presynaptic protein Piccolo

Mol Psychiatry
PMCID: 2717726
PMID: 19065144
DOI: 10.1038/mp.2008.125
call_split See protocol

[…] We used two imputation approaches, the SNPMStat method of Lin et al. () to impute 246 additional SNPs in the PCLO region and Abecasis' MACH (v1) to impute 2,037,829 autosomal SNPs with R2 ≥ 0.5 (a cutoff that removes ∼90% of SNPs with unre […]


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SNPMStat institution(s)
Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

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