added: full support for reference panel based chunking added: improved support for ShapeIT phased haplotypes improved performance (Thanks to David Hinds - see also minimac2 for the full set of performance improvements) all variants (SNPs, InDels, SVs) in the reference VCF will be imputed - independent from the FILTER column setting The latter version uses the OpenMP protocol to support multi-threading, resulting in faster throughput.īE AWARE: since this version of minimac runs in parallel the order of samples in the output files (*dose, *haps.) will vary between runs. The current version of minimac comes in two flavours, minimac and minimac-omp. If you use this beta version, please be sure to stop by the MaCH download page and fill out the registration form, so that we can let you know when an official release is available and keep you updated with respect to any bug fixes. The current version of minimac should be stamped 2013.7.17 - if your version shows a different version number or date stamp when it runs, it is not current. 3.2.5 Additional Sources of InformationĪ binary Linux (64 bit) version of minimac is available from here and source code from here.3.1 Estimating Haplotypes for Your Sample.Imputation server - We are running imputation (and pre-phasing) for you!.Minimac Diagnostics - Summary of diagnostics for imputation performance generated by minimac.Minimac Command Reference - Summary of minimac options.Minimac: 1000 Genomes Imputation Cookbook - Cookbook instructions for 1000 Genomes Imputation with Minimac.Minimac: Tutorial - A short minimac tutorial.Minimac - This page, the main minimac page.There are several minimac related pages on this wiki. The second, "mac", is short hand for MaCH, our widely used algorithm for genotype imputation. The first, "mini", refers to the modest amount of computational resources it requires. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. Minimac is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. You may want to learn about new and improved Minimac4.
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