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/20200701_122138/output/Processed_MAF/
		-tokheimMAF_maftools.maf
Step 2 : Generate ANNOVAR files:
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20200701_122138/output/ANNOVAR_EA/
		-KIRP
		-KIRC
		-OV
		-GBM
		-LUAD
		-LUSC
		-BRCA
		-LGG
		-COAD
		-LAML
		-PRAD
		-KICH
		-READ
		-CESC
		-BLCA
		-SKCM
		-HNSC
		-PAAD
		-LIHC
		-UCEC
		-THCA
		-STAD
Step 3 : Generate gene profile files:
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20200701_122138/output/Gene_profiles/
		-BLCA
		-LAML
		-LIHC
		-PRAD
		-SKCM
		-LGG
		-STAD
		-OV
		-GBM
		-KIRC
		-LUSC
		-BRCA
		-KICH
		-THCA
		-HNSC
		-KIRP
		-LUAD
		-READ
		-COAD
		-PAN
		-UCEC
		-CESC
		-PAAD
Step 4.1 : Generate CI files - sLOF/sGOF
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20200701_122138/output/CI_results/sLOFsGOF/
Step 4.2 : Generate CI files - Run CI analysis
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20200701_122138/output/CI_results/
		-BLCA
		-LAML
		-LIHC
		-PRAD
		-SKCM
		-LGG
		-STAD
		-OV
		-GBM
		-KIRC
		-LUSC
		-BRCA
		-KICH
		-THCA
		-HNSC
		-KIRP
		-LUAD
		-READ
		-COAD
		-PAN
		-UCEC
		-CESC
		-PAAD
Step 5 : Get significantly mutated genes
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20200701_122138/output/Significant_genes/
		-LIHC
		-THCA
		-KICH
		-SKCM
		-KIRP
		-PAAD
		-BRCA
		-CESC
		-GBM
		-UCEC
		-COAD
		-LGG
		-LUSC
		-LUAD
		-HNSC
		-LAML
		-PAN
		-READ
		-KIRC
		-PRAD
		-BLCA
		-OV
		-STAD
Step 6 : Generate sLOF/sGOF plot
	- Output folder: /lab/cedar/home/hgovinda/Cohort-Integration/CohortIntegration/Data/20200701_122138/output/Significant_genes_plots/
		-LIHC_allGene