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  vcf2gwas: python API for comprehensive GWAS analysis using GEMMA

Vogt, F., Shirsekar, G., & Weigel, D. (2021). vcf2gwas: python API for comprehensive GWAS analysis using GEMMA. Bioinformatics, 38(3), 839-840. doi:10.1093/bioinformatics/btab710.

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 Creators:
Vogt, F1, Author           
Shirsekar, G1, Author           
Weigel, D1, Author           
Affiliations:
1Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375790              

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 Abstract: Motivation: Genome-wide association study (GWAS) requires a researcher to perform a multitude of different actions during analysis. From editing and formatting genotype and phenotype information to running the analysis software to summarizing and visualizing the results. A typical GWAS workflow poses a significant challenge of utilizing the command-line, manual text-editing and requiring knowledge of one or more programming/scripting languages, especially for newcomers.

Results: vcf2gwas is a package that provides a convenient pipeline to perform all of the steps of a traditional GWAS workflow by reducing it to a single command-line input of a Variant Call Format (VCF) file and a phenotype data file. Additionally, all the required software is installed with the package. vcf2gwas also implements several useful features enhancing the reproducibility of GWAS analysis.

Availability and implementation: The source code of vcf2gwas is available under the GNU General Public License. The package can be easily installed using conda. Installation instructions and a manual including tutorials can be accessed on the package website at https://github.com/frankvogt/vcf2gwas.

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 Dates: 2021-10
 Publication Status: Issued
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 Rev. Type: -
 Identifiers: DOI: 10.1093/bioinformatics/btab710
PMID: 34636840
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 38 (3) Sequence Number: - Start / End Page: 839 - 840 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991