gbs (Genotyping by Sequencing)
Python and R tools for handling genotyping by sequencing data. The UNEAK pipeline HapMap (hmp.txt) and HapMapCount (hmc.txt) files act as input.
gbs.py: This file contains the function calls for the main pipeline (read-depth filtering, sorting according to abundance of data, HWE-exact-probabilities, expected heterozygosity and some data-conversion). This script calls functions, defined in gbs_mod.py. Follow the script from an IDE or in the console. Import all necessary modules and read in the hmp and hmc files. (Rename your files appropriately or change the script)
gbs_mod.py: Contains the functions for gbs.py
replica.py: This file contains the functions to calculate mismatch rates. It calls functions that are defined in gbs_mod.py.
plot.r: contains some barplot and violinplot calls for R.
plot_locus.py: contains some basic distribution plotting calls for python/matplotlib.