BackgroundTo 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.FindingsGenotype 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.ConclusionsGH 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.
Purpose: To evaluate the accuracy and reproducibility of aortic pulse wave velocity (PWV) assessment by in-plane velocity-encoded magnetic resonance imaging (MRI).
Materials and Methods:In 14 patients selected for cardiac catheterization on suspicion of coronary artery disease and 15 healthy volunteers, PWV was assessed with multislice two-directional in-plane velocity-encoded MRI (PWV i.p. ) and compared with conventionally assessed PWV from multisite one-directional through-plane velocityencoded MRI (PWV t.p. ). In patients, PWV was also obtained from intraarterially acquired pressure-time curves (PWV pressure ), which is considered the gold standard reference method. In volunteers, PWV i.p. and PWV t.p. were obtained in duplicate in the same examination to test reproducibility. Conclusion: PWV i.p. is an improvement over conventional PWV t.p. by showing higher agreement as compared to the gold standard (PWV pressure ) and higher reproducibility for repeated MRI assessment.
MOLGENIS Research is freely available (open source software). It can be installed from source code (see http://github.com/molgenis), downloaded as a precompiled WAR file (for your own server), setup inside a Docker container (see http://molgenis.github.io), or requested as a Software-as-a-Service subscription. For a public demo instance and complete installation instructions see http://molgenis.org/research.
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