RAREMETAL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RAREMETAL
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Tool usage distribution map

This map represents all the scientific publications referring to RAREMETAL per scientific context
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Associated diseases

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Popular tool citations

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Protocols

RAREMETAL specifications

Information


Unique identifier OMICS_00243
Name RAREMETAL
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

Subtool


  • RAREMETALWORKER

Download


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Versioning


No version available

Documentation


Maintainers


  • 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 citations

 (21)
library_books

Exome chip meta analysis identifies novel loci and East Asian specific coding variants contributing to lipid levels and coronary artery disease

2017
Nat Genet
PMCID: 5899829
PMID: 29083407
DOI: 10.1038/ng.3978

[…] lar 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 in a quantile–quanti […]

call_split

Exome wide association study of plasma lipids in >300,000 individuals

2017
Nat Genet
PMCID: 5709146
PMID: 29083408
DOI: 10.1038/ng.3977
call_split See protocol

[…] s.From each study, we collected single variant score statistics and their covariance matrix for variants in sliding windows across the genome. Summary association test statistics were generated using RAREMETALWORKER or RVTESTS. Using summary association statistics collected from each study, we performed meta-analysis of single variant association tests using the Mantel-Haenszel test and constructe […]

library_books

CNV association meta analysis in 191,161 European adults reveals new loci associated with anthropometric traits

2017
Nat Commun
PMCID: 5622064
PMID: 28963451
DOI: 10.1038/s41467-017-00556-x

[…] 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:βMeta=∑cpgc∑cgc2-Nc*gc¯2 seMeta=1∑cgc2-Nc*gc¯2where gc2 is the su […]

library_books

Analysis of potential protein modifying variants in 9000 endometriosis patients and 150000 controls of European ancestry

2017
Sci Rep
PMCID: 5595920
PMID: 28900119
DOI: 10.1038/s41598-017-10440-9

[…] d 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 for each varia […]

library_books

Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease

2017
Nat Genet
PMCID: 5844224
PMID: 28869590
DOI: 10.1038/ng.3943

[…] ild 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. In the meta […]

library_books

Exome wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling

2017
Hum Mol Genet
PMCID: 5886170
PMID: 28973304
DOI: 10.1093/hmg/ddx328

[…] We prepared genotype data for gene-based association testing using EPACTS (v3.2.3; http://genome.sph.umich.edu/wiki/EPACTS; date last accessed August 15, 2017) to annotate variants. We used RAREMETALWORKER (v4.13.5) () to generate score statistics and covariance information based on individual markers in each study; population structure was controlled for using a genetic relatedness matr […]


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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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