Currently, the handling of mutation records with the 5'Flank mutation type differs based on whether custom filtered mutations are specified. Here’s the observed behavior:
Default Filtered Mutations:
When using the default filtered mutations, the 5'Flank mutation is selected, and the protein change field is set to "Promoter" specifically for the TERT gene. This is achieved via a check against whiteListGenesForPromoterMutations (see MutationFilter.java#L150).
Custom Filtered Mutations:
When a custom mutation filter list is applied, the whiteListGenesForPromoterMutations check is skipped, resulting in different handling for 5'Flank mutations (see MutationFilter.java#L133).
This asymmetry in behavior seems unintended and could lead to inconsistent mutation handling depending on the filter setup.
Currently, the handling of mutation records with the 5'Flank mutation type differs based on whether custom filtered mutations are specified. Here’s the observed behavior:
Default Filtered Mutations: When using the default filtered mutations, the 5'Flank mutation is selected, and the protein change field is set to "Promoter" specifically for the TERT gene. This is achieved via a check against whiteListGenesForPromoterMutations (see MutationFilter.java#L150).
Custom Filtered Mutations: When a custom mutation filter list is applied, the whiteListGenesForPromoterMutations check is skipped, resulting in different handling for 5'Flank mutations (see MutationFilter.java#L133).
This asymmetry in behavior seems unintended and could lead to inconsistent mutation handling depending on the filter setup.