MIP_segments_bash

Input data and bash scripts to create coordinates of segments on reference sequences.<br>Usage:1. decompres and untar .gz files2. run get_ind_cov.sh - produces coverage files for each species2. run segments_on_MIPs.sh - produces for each species .bed file with coordinates on segments on MIPs. This file is used as input to R script R_microhaplotypes.R<br>Files:- references.tar.gz - reference sequences for each species; introns are indicated with N runs- MIPnumber_min20cov.txt.gz - .bed file with coordinates of each MIP in each species on reference- MIP_beds.tar.gz - .bed files for each species containing coordinates of MIPs on references (were generated from MIPnumber_min20cov.txt)- MIPcoverage_Ind.txt.gz - per MIP per individual coevareg for each individual and species<br>- vcfs.tar.gz - per MIP per species .vcf files<br><br><br>