VCFViz

The program can be run in any environment that has: samtools, pandas and an Excel writer (openpyxl) if a sumamry excel file of the html information is needed.

The environment yaml can set up the environment for you, to create it you can simply run: conda env create -f environment.yaml

then install the program with pip install . (Make sure your in the setup directory)

TODO

• Add average to heat map of altfreq
• Add selcted average to heat map of altfreq for mutations toggled to true input sheet
• Highlight selected mutations based off of input sheet markup
• When same mutations is listed in the same lineage one is dropped

Run

To run:

• more information to come, but the run command is VCFViz
• Run options will be elaborated on in the future