HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS.

Autor:	Slaten ML; Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA., Chan YO; Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA., Shrestha V; Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA., Lipka AE; Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA., Angelovici R; Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2020 Nov 01; Vol. 36 (17), pp. 4655-4657.
DOI:	10.1093/bioinformatics/btaa589
Abstrakt:	Motivation: Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis, such as outlier removal, data transformation and calculation of Best Linear Unbiased Predictions or Best Linear Unbiased Estimates. In addition, post-GWAS analysis, such as haploblock analysis and candidate gene identification, is lacking. Results: Here, we present Holistic Analysis with Pre- and Post-Integration (HAPPI) GWAS, an open-source GWAS tool able to perform pre-GWAS, GWAS and post-GWAS analysis in an automated pipeline using the command-line interface. Availability and Implementation: HAPPI GWAS is written in R for any Unix-like operating systems and is available on GitHub (https://github.com/Angelovici-Lab/HAPPI.GWAS.git). Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze:	MEDLINE
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