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oncokb / oncokb-annotator

Annotates variants in MAF with OncoKB annotation.
GNU Affero General Public License v3.0
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MAF annotator annotates Likely-oncogenic mutation as Unknown #202

Closed andreyurch closed 1 year ago

andreyurch commented 1 year ago

Dear team,

I found a strange behaviour of MafAnnotator.py (3.3.2).

I have a mutation

CYLD 16 50825488 50825488 Nonsense_Mutation SNP C C T c.2119C>T p.Q707*

After python3 oncokb-annotator-3.3.2/MafAnnotator.py -q Genomic_Change -i MUT.txt LNM -r GRCh37 I have:

Unknown   Unknown

But it is oncogenic according to the Genome Nexus and OncoKB databases: https://www.genomenexus.org/variant/16:g.50825488C%3ET

The same is happening for some (not all, minority) of my variants:

CYLD 16 50826564 50826565 Frame_Shift_Ins INS - - A c.2289_2290insA p.K764fs
CYLD 16 50828286 50828286 Frame_Shift_Del DEL A A - c.2624delA p.Y875fs
CYLD 16 50828288 50828290 In_Frame_Del DEL GGG GGG - c.2626_2628delGGG p.G876del
CYLD 16 50811826 50811826 Nonsense_Mutation SNP C C A c.1103C>A p.S368*
CYLD 16 50827564 50827564 Missense_Mutation SNP T T C c.2449T>C p.C817R
andreyurch commented 1 year ago

I apologise, it was my mistake