title: Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.
abstract: 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.
  
  
  RESULTS
  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 http://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.
authors.affiliation: University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands. patrickdeelen@gmail.com.
authors.forename: Patrick
authors.initials: P
authors.lastname: Deelen
authors.forename: Marc Jan
authors.initials: MJ
authors.lastname: Bonder
authors.forename: K Joeri
authors.initials: KJ
authors.lastname: van der Velde
authors.forename: Harm-Jan
authors.initials: HJ
authors.lastname: Westra
authors.forename: Erwin
authors.initials: E
authors.lastname: Winder
authors.forename: Dennis
authors.initials: D
authors.lastname: Hendriksen
authors.forename: Lude
authors.initials: L
authors.lastname: Franke
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
mesh_terms: D019295:Computational Biology / Q000379:methods*; D055106:Genome-Wide Association Study / Q000706:statistics & numerical data*; D023281:Genomics / Q000706:statistics & numerical data*; D005838:Genotype; D006801:Humans; D020407:Internet; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results