SKAT statistics

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SKAT specifications


Unique identifier OMICS_07454
Alternative name SNP-set (Sequence) Kernel Association Test
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes


No version available


  • person_outline Seunggeun (Shawn) Lee

Publications for SNP-set (Sequence) Kernel Association Test

SKAT citations


Exact association test for small size sequencing data

BMC Med Genomics
PMCID: 5918458
PMID: 29697368
DOI: 10.1186/s12920-018-0344-z

[…] d, burden tests aggregate information from all rare variants in a specific genomic region into a single summary variable, and obtain p-values through the chi-square distribution or Hoteling’s t-test. SKAT is based on a regression model, using a variance-component test to evaluate the significance of specific genes, using score test statistics, which follow the asymptotic chi-square distribution, u […]


WISARD: workbench for integrated superfast association studies for related datasets

BMC Med Genomics
PMCID: 5918457
PMID: 29697360
DOI: 10.1186/s12920-018-0345-y
call_split See protocol

[…] subjects. In addition, gene-level tests are often used for association analysis with rare variants, and cover the combined and multivariate collapsing test [], variable threshold (VT) method [], and SKAT [, ], etc. In particular, most of gene-level tests were limited to population-based samples, and few approaches available for family-based samples. PEDCMC [], FARVAT [], mFARVAT [], and FARVATx [ […]


New Common and Rare Variants Influencing Metabolic Syndrome and Its Individual Components in a South Korean Population

Sci Rep
PMCID: 5890262
PMID: 29632305
DOI: 10.1038/s41598-018-23074-2
call_split See protocol

[…] ts: Gene-based analysis for single phenotype3logit(pi)=β0+∑kγkzik+∑jβjxij4yi=β0+∑kγkzik+βjxij+∑jβjxij+ϵiFor rare variant analysis, for single phenotypes, we used the Sequence Kernel Association Test (SKAT). For the binary phenotype of MetS, LR was used as given in equation (), and the linear regression was fit to equation (), for each continuous component of MetS. Unlike common variant analysis, i […]


Evaluation of Gene Based Family Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease

Front Neurosci
PMCID: 5893779
PMID: 29670507
DOI: 10.3389/fnins.2018.00209
call_split See protocol

[…] ach one of these scenarios we evaluated the performance of the different gene-based methods (collapsing, variance-component, and transmission disequilibrium) from the following family-based packages: SKAT (Wu et al., ), FSKAT (Yan et al., ), GSKAT (Wang et al., ), RVGDT (He et al., ), EPACTS (, FarVAT (Choi et al., ), PedGene (Schaid et al., ), RareIBD (Sul […]


GxGrare: gene gene interaction analysis method for rare variants from high throughput sequencing data

BMC Syst Biol
PMCID: 5861485
PMID: 29560826
DOI: 10.1186/s12918-018-0543-4

[…] that the MAF based collapsing method showed the best overall performance in the results of simulation data, in terms of power (while preserving type I error), in our simulation studies comparing SPA, SKAT and the three proposed collapsing methods explained in detail in our methods section. This result was somewhat surprising in that the simple collapsing of variants with similar MAFs were able to […]


Advances in the Genetics of Hypertension: The Effect of Rare Variants

Int J Mol Sci
PMCID: 5877549
PMID: 29495593
DOI: 10.3390/ijms19030688

[…] idual variant tests are underpowered to detect rare variant effects because of the low allele frequencies. Statistical methods to test for rare variants can be categorized as burden approach [,,] and SKAT (Sequence Kernel Association Test) approach [,]. Burden tests assume all rare variants in the target region have effects on the phenotype in the same direction and of similar magnitude [,], but t […]


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SKAT institution(s)
Department of Biostatistics, Columbia University, New York, NY, USA

SKAT review

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simon boutry

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Great package offering a huge diversity of region-based test for association testing