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

BMC Res Notes. 2014 Dec 11;7:901. doi: 10.1186/1756-0500-7-901.


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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Genome-Wide Association Study / statistics & numerical data*
  • Genomics / statistics & numerical data*
  • Genotype
  • Humans
  • Internet
  • Linkage Disequilibrium
  • Polymorphism, Single Nucleotide*
  • Reproducibility of Results