Usage: python [CohortInteg code name] [input folder] [output folder] [qva]
0.1
Step 1 : Process maf files:
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/Processed_MAF/
		-pancan-mutation-set-from-Tokheim-2016-LIHConly_MAF.maf
Step 2 : Generate ANNOVAR files:
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/ANNOVAR_EA/
		-BRCA
Step 3 : Generate gene profile files:
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/Gene_profiles/
		-BRCA
		-PAN
Step 4.1 : Generate CI files - sLOF/sGOF
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/CI_results/sLOFsGOF/
Step 4.2 : Generate CI files - Run CI analysis
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/CI_results/
		-BRCA
		-PAN
Step 5 : Get significantly mutated genes
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/Significant_genes/
		-BRCA
		-PAN
Step 6 : Generate sLOF/sGOF plot
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20220126_082604/output/Significant_genes_plots/
		-PAN_allGene