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A pipeline tool for genotype imputation for the grid and local cluster environments. The automation includes the following steps: genome build liftover, genotype phasing (SHAPEIT2), quality control, sample, and chromosomal chunking, and genotype imputation (IMPUTE). Molgenis-impute utilizes MOLGENIS-compute (see 'links') for submission and monitoring of tasks. Requires: wget or curl, tar, unzip, bunzip2, g++, java 1.6 or higher, python 2.7, and numpy.


DNA; Genetics; Genotype and phenotype


  • Operation: Imputation
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux; Mac OS X
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 0.9.1
  • Credit: Ubbo Emmius fund, Netherlands Organization for Scientific Research
  • Contact: alexandros.kanterakis _at_
  • Collection: -


Kanterakis A, Deelen P, van Dijk F, Byelas H, Dijkstra M, Swertz MA "Molgenis-impute: imputation pipeline in a box." BMC Res Notes. 2015 Aug 19;8:359.
PMID: 26286716
PMCID: PMC4541731

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