Instructions_for_running_code.txt

##To reproduce all of the results from this study, run the following code in this order:

1) The code for generating the SARS-CoV-2 Incremental Database, which is present in the folder "IncDB_code" and explained in the file "Workflow_for_IncDB_code".

2) main_python_script.py (Python 3 script)

3) main_R_script.R (R script)

This reproduces all results and figures for this study.

Also included in this directory is the python3 script sarscov2blacklister.py - this script takes the following arguments:
The file path to the inut VCF you would like to annotate (-i)
The file path to Freeman_full_blacklist.xlsx (-b)
The script outputs a modified VCF file with the altered ending ".bl.vcf" instead of ".vcf" to avoid overwriting the original VCF
The modified VCF has an additional two columns "BLACKLIST?" and "REASON" which state whether each variant was blacklisted in the study (mask, caution or not_blacklisted), and why, if it was blacklisted.
The script requires the python modules vcf, csv, sys and getopt