RICOPILI automates computationally costly genotype imputation with an optimized routine for high-performance computing (HPC) environments (Supplementary Section S3 and Fig. S4). This module aligns genotype data to the imputation reference, pre-phases haplotypes and executes imputation. Users have the option to: Impute genotypes to the 1000 Genomes (1000 Genomes Project Consortium et al., 2015) or Haplotype Reference Consortium panel (McCarthy et al., 2016);Perform pre-phasing with Eagle (Loh et al., 2016) or SHAPEIT (Delaneau et al., 2011);Perform imputation with IMPUTE (Bycroft et al., 2018; Howie et al., 2009) or Minimac (Das et al., 2016; Howie et al., 2012).
