Missing mutation types

[onursumer]

Looks like we are still missing some of the mutation types:

OncoKB mutation type	MutationMapper mutation type
inframe_insertion	in_frame_ins
inframe_deletion	in_frame_del
frameshift_variant	frameshift
splice_region_variant	splice_site
feature_truncation	truncating
stop_gained	truncating
stop_lost	truncating
initiator_codon_variant	truncating
synonymous_variant	other
any	other

[onursumer]

@jjgao @JiaoJiao123 If we directly map stop_gained, stop_lost, initiator_codon_variant, etc. to truncating mutation, their display value in the table will be Truncating. Is this what we want?

Maybe we should display them as Stop Gain, Stop Lost, etc. but just classify them as truncating mutations. What do you think?

[jjgao]

We can do the following mapping accroding to the TCGA MAF standard (https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification).

stop_gained => Nonsense_Mutation
stop_lost => Nonstop_Mutation
initiator_codon_variant => Translation_Start_Site
synonymous_variant => Silent

feature_truncation is truncating