AUTHORS: D. Wittenburg, N. MelzerDATE: October 13, 2025OBJECTIVE: Create a genetic map and interactively visualise the outcomeSOURCE: The R package CLARITY is available athttps://github.com/nmelzer/CLARITYAn online version of CLARITY is available athttps://nmelzer.shinyapps.io/clarity/INSTRUCTIONS:1. The pipeline for creating a male genetic map from genotypes of paternal half-siblings with the    hsrecombi approach (Hampel et al. 2018) is available in subfolder makefile_for_<real/sim>_data.    The pipeline requires make version >= 4.3; this version allows for grouped targeting.   Ensure that required R packages have been installed (hsrecombi >=1.0.0, ggplot2; optional:    AlphaSimR), then call "make all". For each chromosome i, genetic and physical positions are    stored as a list in geneticpositions_chr<i>.Rdata. Further interim results are available.2. Additionally, sex-specific and average genetic maps employing all genotypes can be estimated    with the LINKPHASE3 approach (Druet & George 2015). To this end, run "run_linkphase.R" in the   same working directory as "make all" (requires R packages magrittr, hsrecombi, dplyr, data.table).3. To prepare input data for the R-Shiny app CLARITY version >= 3.0.0 in the required format, run    "prepare_data_rshiny.R" in the same working directory as "make all" (requires R packages    magrittr, hsrecombi, dplyr). The output Rdata will then be content of folder    CLARITY/inst/extdata. Note that, unless working with nchr = 29 bovine autosomes, modifications   to the app become necessary.