cBioPortal / mutation-mapper

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Missing mutation types #60

Open onursumer opened 8 years ago

onursumer commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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