pseudocode_analysis.txt

##Sept 30, 2020
## Pseudocode for analysis


Using file of unique germline variants in a given tissue cohort:

	Run variants through OpenCravat to get Revel score and pathogenic interpretations from ClinVar, establish cut offs from paper (for missense variants)
	Run variants through BayesDel (Bing Feng, Utah, for indel variants)
	Identify variants that result in a loss of function mutation (using cut offs for Revel, tbd for BayesDel)

Using file with data per individual, per variant:
	
	For each gene, use this file to identify the individuals who have LOF mutations (positions already identified above)

Using file of somatic variants in a given tissue cohort:

	For each gene, match individuals (sample IDs) to view both germline data and somatic data in one file
	Identify individuals who have both LOF germline mutation and somatic variant with gistic score of either -1 or -2
		Add these individuals to a two hit group (either list or separate file)
	Identify individusals who have either LOF germline mutation or somatic variant with gistic score of eitehr -1 or -2
		Add these individuals to an at least one hit group (either list or separate file)
	Identify individuals who are not in either two hit or one hit group

Using somatic mutational score data:
	Compare somatic mutational scores in individuals with two hits, one hit, and no hits.