Phasing and imputation require the use of genetic recombination maps, typically distributed with phasing and imputation tools. Recently, SHAPEIT4 and IMPUTE5 have been released with genetic maps that, as I here show, differ from those used by SHAPEIT2, IMPUTE2 and EAGLE2. This article explores these differences to shed light on potential compatibility and comparability issues.
The analysis and figures are based on the genetic maps distributed both with SHAPEIT4, namely
and with EAGLE2, namely
Copyright (c) 2020 Ph.D. Hugo Gabriel Eyherabide All files in this repository are licensed under the GPLv3 license (see LICENSE).