I would like to have some (semi-official) translation table of TransVar annotated variant_class into MAF(Mutation Annotation Format) class. Could you consider to correct or/and add this preliminary info into TransVar documentation?
... and what about the following mutations? How to identify them in TransVar output?
5'Flank, 3'Flank, RNA, Targeted_Region, De_novo_Start_InFrame, De_novo_Start_OutOfFrame
I would like to have some (semi-official) translation table of TransVar annotated variant_class into MAF(Mutation Annotation Format) class. Could you consider to correct or/and add this preliminary info into TransVar documentation?
TransVar = MAF
3-UTRBlockSubstitution = 3'UTR 3-UTRDeletion = 3'UTR 3-UTRInsertion= 3'UTR 3-UTRSNV = 5'UTR 5-UTRBlockSubstitution = 5'UTR 5-UTRDeletion = 5'UTR 5-UTRInsertion = 5'UTR 5-UTRSNV = 5'UTR CdsStartBlockSubstitution = Translation_Start_Site CdsStartDeletion = Translation_Start_Site CdsStartInsertion = Translation_Start_Site CdsStartSNV = Translation_Start_Site CdsStopBlockSubstitution = Nonsense_Mutation CdsStopDeletion = Nonstop_Mutation CdsStopInsertion = Nonsense_Mutation CdsStopSNV = Silent Frameshift = Frame_Shift_InDel # how to separate Frame_Shift_Del / Frame_Shift_Ins ? InFrameDeletion = In_Frame_Del InFrameInsertion = In_Frame_Ins IntergenicBlockSubstitution = IGR IntergenicDeletion = IGR IntergenicInsertion = IGR IntergenicSNV = IGR IntronicBlockSubstitution = Intron IntronicDeletion = Intron IntronicInsertion = Intron IntronicSNV = Intron Missense = Missense_Mutation MultiAAMissense = Missense_Mutation Nonsense = Nonsense_Mutation SpliceAcceptorBlockSubstitution = Splice_Site SpliceAcceptorDeletion = Splice_Site SpliceAcceptorInsertion = Splice_Site SpliceAcceptorSNV = Splice_Site # or Splice_Region? SpliceDonorBlockSubstitution = Splice_Site SpliceDonorDeletion = Splice_Site SpliceDonorInsertion = Splice_Site SpliceDonorSNV = Splice_Site # or Splice_Region? Synonymous = Silent Unclassified = UNKNOWN UnclassifiedBlockSubstitution = UNKNOWN UnclassifiedDeletion = UNKNOWN
... and what about the following mutations? How to identify them in TransVar output? 5'Flank, 3'Flank, RNA, Targeted_Region, De_novo_Start_InFrame, De_novo_Start_OutOfFrame