Paul Wolf Lab, Utah State University
Python R
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
HapMap.hmc.txt.tar.gz
HapMap.hmp.txt.tar.gz
README.md
fst_hierfstat.r
gbs.py
gbs_mod.py
locus_plot.py
plot.r
replica.py

README.md

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

  • 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.

BUILD NOTES