Genotype imputation has become a standard tool in genetics, but performing this analysis correctly requires considerable expertise and is time and labor intensive. We developed an impute2-based genotype imputation workflow that greatly simplifies the process of imputation and achieves a significant speedup of imputation using multiple CPUs on a computer cluster. The user simply provides a genotype dataset and the workflow implements detailed steps of matching the strand of the input genotypes and reference, smart segmentation of the genome and generation of QC metrics.
Availability and implementation: The workflow works on the two most popular cluster management systems, Sun Grid Engine (SGE) and Portable Batch System (PBS). It is available under the GNU public license.
Authors: Hugues Sicotte, Naresh Prodduturi
Hugues Sicotte, Ph.D.
Page last modified: April 1, 2016