INTRODUCTION
Jairo Rocha, 2023.
Scripts are licensed under the Creative Commons by NC-SA license.
Cancer Epistatic Genes Finder (CEG-Finder) scripts.
This script produces gene pairs related to cancer tumor.
Download the .vcf files in the annotations/COAD/vcf directories.
Vcf files must be normal tumor mutation pairs.
HOW TO RUN
The use of nohup is recommended so that the process do not die even when the console gets disconnected.
nohup ./Script
Input files are VCF files from TCGA to be processed with Annovar. First with table_annovar procedure Then with convert2annovar Finally with annotateVariation
If we want to filter:
python SNPFilterAnnovarFiles.py table_annovar_dir files_list.txt 19 -n 20 --maf 0.005 --filtMut --minAD 10 --minRatioAD_DP 0.05
Create SNP x subjects matrix
python SNPStumorAndnormalFilteredFiles.py directory_of_inputFiles files_list -o outFile --file type_of_file --maf 0.005 --minAD 10 --minRatioAD_DP 0.05
CREATE GENE MATRIX FROM SNP DATA
After the three special cells in the contingency tables of all gene pairs are analyzed, the output is in 3cell/dataCOAD/GPairsPvaluesTop