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Open AccessJournal ArticleDOI

RAREMETAL: fast and powerful meta-analysis for rare variants.

Shuang Feng, +4 more
- 01 Oct 2014 - 
- Vol. 30, Iss: 19, pp 2828-2829
TLDR
RAREMETAL facilitates analyses of individual studies, accommodates a variety of input file formats, handles related and unrelated individuals, executes both single variant and burden tests and performs conditional association analyses.
Abstract: 
Summary: RAREMETAL is a computationally efficient tool for meta-analysis of rare variants genotyped using sequencing or arrays. RAREMETAL facilitates analyses of individual studies, accommodates a variety of input file formats, handles related and unrelated individuals, executes both single variant and burden tests and performs conditional association analyses. Availability and implementation: http://genome.sph.umich.edu/wiki/RAREMETAL for executables, source code, documentation and tutorial. Contact: ude.hcimu@hpsgnefs or ude.hcimu@olacnog

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Citations
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Journal ArticleDOI

Rare and low-frequency coding variants alter human adult height

Magic Investigators
- 09 Feb 2017 - 
TL;DR: In this paper, the authors report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2'centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants.
Journal ArticleDOI

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

Dajiang J. Liu, +288 more
- 30 Oct 2017 - 
TL;DR: It is found that beta-thalassemia trait carriers displayed lower TC and were protected from coronary artery disease (CAD), and only some mechanisms of lowering LDL-C appeared to increase risk for type 2 diabetes (T2D); and TG-lowering alleles involved in hepatic production of TG-rich lipoproteins tracked with higher liver fat, higher risk for T2D, and lower risk for CAD.

Rare and low-frequency coding variants alter human adult height

Eirini Marouli, +370 more
TL;DR: The results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
Journal ArticleDOI

RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.

Xiaowei Zhan, +4 more
- 01 May 2016 - 
TL;DR: RVTESTS is developed, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related individuals and provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection.

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

Dajiang J. Liu, +226 more
References
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Journal ArticleDOI

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Petr Danecek, +11 more
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TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
Journal ArticleDOI

METAL: fast and efficient meta-analysis of genomewide association scans.

Cristen J. Willer, +2 more
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TL;DR: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies.
Journal ArticleDOI

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Gonçalo R. Abecasis, +3 more
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TL;DR: The multipoint engine for rapid likelihood inference (Merlin) is a computer program that uses sparse inheritance trees for pedigree analysis; it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.
Journal ArticleDOI

Variance component model to account for sample structure in genome-wide association studies

Hyun Min Kang, +6 more
- 01 Apr 2010 - 
TL;DR: A variance component approach implemented in publicly available software, EMMA eXpedited (EMMAX), that reduces the computational time for analyzing large GWAS data sets from years to hours is reported.
Journal ArticleDOI

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

Michael C. Wu, +5 more
- 15 Jul 2011 - 
TL;DR: The sequence kernel association test (SKAT) is proposed, a supervised, flexible, computationally efficient regression method to test for association between genetic variants (common and rare) in a region and a continuous or dichotomous trait while easily adjusting for covariates.
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