MetaSKAT protocols

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MetaSKAT specifications

Information


Unique identifier OMICS_00241
Name MetaSKAT
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MetaSKAT

MetaSKAT in pipeline

2016
PMCID: 5861862
PMID: 27154906
DOI: 10.1093/gerona/glw074

[…] test; then the heterogeneity between men and women was assessed by use of the above-described meta-analysis procedures. meta-analysis of the results from the skat-o test was carried out by use of metaskat ()., to verify that the snps identified as being associated with extreme longevity were also associated with overall life span, we performed kaplan–meier survival analysis of 2,274 quality […]


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MetaSKAT in publications

 (6)
PMCID: 5735917
PMID: 29257133
DOI: 10.1038/sdata.2017.179

[…] criteria for deleteriousness, and the ptv+missense mask included variants in the ptv+nsbroad mask as well as those with maf<1% annotated as missense., we performed gene-level analysis using the metaskat software package (v0.32), employing the skat v0.93 library to perform a skat-o analysis within each ancestry group as well as across all ancestry groups via meta-analysis. within […]

PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] with comprehensive third-generation long-read sequencing. we characterized the abca7 coding sequence with next-generation sequencing in 928 eoad patients and 980 matched control individuals. with metaskat rare variant association analysis, we observed a fivefold enrichment (p = 0.0004) of ptc mutations in eoad patients (3%) versus controls (0.6%). ten novel ptc mutations were only observed […]

PMCID: 5034897
PMID: 27398621
DOI: 10.1038/nature18642

[…] using high-quality genotype calls (gq>20) for all samples passing extended qc. we considered a variant to have maf<1% if maf estimates for every ancestry group were <1%., we used the metaskat r package (v0.32) with the skat v0.93 library to perform skat-o analysis within each ancestry, and in meta-analysis. within each ancestry group, we analyzed genotype dosages with adjustment […]

PMCID: 5861862
PMID: 27154906
DOI: 10.1093/gerona/glw074

[…] test; then the heterogeneity between men and women was assessed by use of the above-described meta-analysis procedures. meta-analysis of the results from the skat-o test was carried out by use of metaskat ()., to verify that the snps identified as being associated with extreme longevity were also associated with overall life span, we performed kaplan–meier survival analysis of 2,274 quality […]

PMCID: 4639776
PMID: 26553438
DOI: 10.1038/srep16286

[…] number of variants in each individual study we performed skat-o test separately for each individual study and combined summary statistics from individual skat results in a meta-analysis using “metaskat” package in r similarly to single-variant analysis we tested for over-dispersion of p-values by generating qq plots and deriving an inflation factor (λ). to account for multiple testing […]


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MetaSKAT institution(s)
Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA

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