microhap_inputs_and_script

Usage:1. Unzip, ungzip untar all files, which should create the appropriate directory structure2. Run microhap_runner_Linux.R - the output should be .rds files that are used by R_microhaplotypes.R

- microhap_runner_Linux.R - R script preparing inputs and running microhaplot package that extracts (micro)haplotypes for each MIP and each individual; this script is normally run on a Linux cluster as it is much faster with multiple cores.
- sams_all_genera.zip - zip archive containing gzipped tar archives with per MIP per individual per species .sam alignments- vcfs_all_genera.zip - zip archive containing gzipped tar archives with per MIP per species .vcf files