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Genotype harmonizer

Genotype harmonizer

A tool for file format conversion for pooled data. It solves unknown strands by aligment of A,T and G,C single nucleotide polymorphisms (SNPs) to a reference sequence, using linkage disequilibrium patterns. Supported file formats: PLINK, binary PLINK, VCF, SHAPEIT2, and Oxford GEN.

Topic

Biology, Genetics, DNA polymorphism

Details

  • Operation: Conversion, Data handling
  • Software interface: Command-line interface
  • Language: Java
  • Operating system: Linux, Mac OS X
  • License: GNU LGPL v3
  • Cost: -
  • Version name: 1.4.20
  • Credit: Deelen P, Bonder MJ, van der Velde KJ, Westra HJ, Winder E, Hendriksen D, Franke L, Swertz MA.
  • Contact: Patrick Deelen patrickdeelen at gmail.com, Morris A Swertz m.a.swertz at gmail.com
  • Collection: -

Publications

Deelen P, Bonder MJ, van der Velde KJ, Westra HJ, Winder E, Hendriksen D, Franke L, Swertz MA "Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration." BMC Res Notes 2014 https://doi.org/10.1186/1756-0500-7-901
PMID: 25495213
PMCID: PMC4307387


Download and documentation




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