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PMID: 23052040 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies.

Bioinformatics (Oxford, England) ·Vol. 28 ·No. 24 ·2012-12-15 ·Pages 3329-31

Gogarten SM, Bhangale T, Conomos MP, Laurie CA, McHugh CP, Painter I, Zheng X, Crosslin DR, Levine D, Lumley T, Nelson SC, Rice K, Shen J, Swarnkar R, Weir BS, Laurie CC

Abstract

GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R's memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation.

MeSH Terms
Genome-Wide Association Study/standards Genotype Humans Polymorphism, Single Nucleotide Quality Control Software
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Gogarten Stephanie M
Department of Biostatistics, University of Washington, Seattle, WA, USA. sdmorris@uw.edu
Bhangale Tushar
Conomos Matthew P
Laurie Cecelia A
McHugh Caitlin P
Painter Ian
Zheng Xiuwen
Crosslin David R
Levine David
Lumley Thomas
Nelson Sarah C
Rice Kenneth
Shen Jess
Swarnkar Rohit
Weir Bruce S
Laurie Cathy C
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Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/bts610
Email
sdmorris@uw.edu
Published
2012-12-15
Epub
2012-00-10
Pages
3329-31
Language
English
Region
England
NLM ID
9808944
PMCID
PMC3519456
Subset
IM
Grants
NHGRI NIH HHS · U01 HG 004446 · United States
NHGRI NIH HHS · U01 HG004446 · United States
NHGRI NIH HHS · U01 HG 005157 · United States
NIGMS NIH HHS · P01 GM099568 · United States
NHGRI NIH HHS · U01 HG005157 · United States
External Links
PubMed source DOI: 10.1093/bioinformatics/bts610 PMC Full Text View journal details
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