RAREMETAL protocols

View RAREMETAL computational protocol

RAREMETAL statistics

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Associated diseases

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RAREMETAL specifications


Unique identifier OMICS_00243
Alternative name RAREMETAL2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Fortran, Shell (Bash)
Computer skills Advanced
Version 4.14.0
Stability Stable
Maintained Yes





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  • person_outline Gonçalo Abecasis <>
  • person_outline Shuang Feng <>

Additional information

https://genome.sph.umich.edu/wiki/RAREMETAL_Documentation A beta version is also available at https://github.com/statgen/Raremetal2.

Publication for RAREMETAL

RAREMETAL in pipeline

PMCID: 5899829
PMID: 29083407
DOI: 10.1038/ng.3978

[…] genezoom, http://genome.sph.umich.edu/wiki/genezoom, exac, http://exac.broadinstitute.org, raremetals, http://genome.sph.umich.edu/wiki/raremetals, rvtests, http://genome.sph.umich.edu/wiki/rvtests, raremetalworker, http://genome.sph.umich.edu/wiki/raremetalworker, author contributions , drafting of the manuscript: x.lu, c.j.w, g.m.p., d.j.l., d.g., k.l.m. project coordination: c.j.w., d.g., […]

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RAREMETAL in publications

PMCID: 5899829
PMID: 29083407
DOI: 10.1038/ng.3978

[…] disease status, cases and controls were analyzed separately., we performed both single variant and gene-level association tests. single variant analyses in each cohort were carried out using either raremetalworker or rvtests, both of which generate single variant score statistics and their covariance matrix between single marker statistics. the test statistics, as visualized […]

PMCID: 5709146
PMID: 29083408
DOI: 10.1038/ng.3977

[…] allele frequency (maf) < 0.1% ()., single-variant association statistics and linkage disequilibrium information summarized across 1 megabase sliding windows were generated from each cohort using raremetalworker or rvtests, software. meta-analyses of single variant and gene-level association tests were performed using raremetals (version 6.0). genomic control values for meta-analysis results […]

PMCID: 5622064
PMID: 28963451
DOI: 10.1038/s41467-017-00556-x

[…] g cohorts ran the exact same pipeline and shared summary statistics with us. an example configuration file can be found in the supplementary note ., we ran fixed effects meta-analysis as described by raremetal. we directly computed the meta β meta and semeta for a given cnv probe from the summary statistics from the multiple cohorts:\documentclass[12pt]{minimal} \usepackage{amsmath} \usepa […]

PMCID: 5595920
PMID: 28900119
DOI: 10.1038/s41598-017-10440-9

[…] errors and a well-calibrated quantile-quantile (q-q) plots (supplementary figures –). tests of association in individual datasets including all endometriosis cases and controls were performed using raremetalworker assuming an additive model. raremetalworker is a forerunner of raremetal, which produces single-variant summary statistics by fitting a linear mixed model. genotype data […]

PMCID: 5844224
PMID: 28869590
DOI: 10.1038/ng.3943

[…] and strand for each study was checked using checkvcf against build37 plus strand. the reference and alternate alleles were aligned with the reference. study specific analyses were conducted using raremetalworker, incorporating the kinship matrix and adjusting for age and sex. in each study, variants with a mac < 10 were removed before meta-analysis. meta-analysis was done in metal. […]

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RAREMETAL institution(s)
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
RAREMETAL funding source(s)
Supported by grants HG-007022 and HG-006513 from National Human Genome Research Institute and HL-117626 from National Heart, Lung, and Blood Institute.


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