Genotype harmonizer: Automatic strand alignment and format conversion for genotype data integration

被引：92

作者：

Deelen P. ^{[1
,2
]}

Bonder M.J. ^{[2
]}

Van Der Velde K.J. ^{[1
,2
]}

Westra H.-J. ^{[2
]}

Winder E. ^{[1
,2
]}

Hendriksen D. ^{[1
,2
]}

Franke L. ^{[2
]}

Swertz M.A. ^{[1
,2
]}

机构：

[1] University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen

[2] University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen

来源：

BMC Research Notes | / 7卷 / 1期

关键词：

GWAS; Imputation; Linkage disequilibrium; Meta-analysis;

D O I：

10.1186/1756-0500-7-901

中图分类号：

学科分类号：

摘要：

Background: To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about which genomic strand is used as reference. Findings: Genotype Harmonizer (GH) is a command-line tool to harmonize genetic datasets by automatically solving issues concerning genomic strand and file format. GH solves the unknown strand issue by aligning ambiguous A/T and G/C SNPs to a specified reference, using linkage disequilibrium patterns without prior knowledge of the used strands. GH supports many common GWAS/NGS genotype formats including PLINK, binary PLINK, VCF, SHAPEIT2 & Oxford GEN. GH is implemented in Java and a large part of the functionality can also be used as Java 'Genotype-IO' API. All software is open source under license LGPLv3 and available from www.molgenis.org/systemsgenetics. Conclusions: GH can be used to harmonize genetic datasets across different file formats and can be easily integrated as a step in routine meta-analysis and imputation pipelines. © 2014 Deelen et al.; licensee BioMed Central.

引用

共 14 条

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