ACCESS CNA call is "RESCUE" even though fold change >2

[kanika-arora]

Description of the bug

Branch used: feature/biometrics_with_fixes_20250818
KRAS amplification with fold change in ACCESS research samples of 7.9, 3, and 4.1 show fc_filter="RESCUED"

Command used and terminal output

Relevant files

/juno/cmo/bergerlab/access_projects/Project_EDD_R01/Project_ALK_ROS_fusion/results_2025-08-19/final_results/copy_number_variants/C-0XKX1M_P-0100449_CNA.csv

System information

No response

[shguturu]

This is a holdover from the R script functionality, which limited analysis of CNAs to this subset of genes:

access.cna.genes = c('AR','BRCA1','BRCA2','CDK4','EGFR','ERBB2','MET','MDM2','MLH1','MSH2','MSH6','MYC')

In this case, KRAS isn't in the ACCESS gene list so it isn't marked as "PASS" but is getting "RESCUED" because it is also in the clinical list.

I can either remove the ACCESS gene list clause altogether and we can assume that any CNA calls pulled from the research CNA templates are all valid ACCESS genes, or I can point the ACCESS gene list to a resource file like these:

/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/MSK-ACCESS-v1_0-target_genes.list
/work/access/production/resources/msk-access/v2.0/regions_of_interest/current/ACCESSv2_all_curated_genes.txt

It seems to me that it should be okay to remove the list completely, but let me know if there is some reasoning I am missing as to why the list is limited.

The SV calls also have a similar filtering clause in the R script and "only SVs implicating any ACCESS SV calling key genes are retained". We should also make a decision here for the NF pipeline, as the gene list is currently using the R script list:
gene.list <- c('ALK','BRAF','ERBB2','EGFR','FGFR1','FGFR2','FGFR3','KIT','MET','NTRK1','NTRK2','NTRK3','PDGFRA','RET','ROS1')