NAME
gbs (Genotyping by Sequencing)
DESCRIPTION
Python and R tools for handling genotyping by sequencing data. The UNEAK pipeline HapMap (hmp.txt) and HapMapCount (hmc.txt) files act as input.
USAGE NOTES
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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)
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gbs_mod.py: Contains the functions for gbs.py
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replica.py: This file contains the functions to calculate mismatch rates. It calls functions that are defined in gbs_mod.py.
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plot.r: contains some barplot and violinplot calls for R.
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plot_locus.py: contains some basic distribution plotting calls for python/matplotlib.
BUILD NOTES