RNA fusions parsing issue?

[northwestwitch]

From a ticket in our support system:

They see 3 fusion variants hitting the genes KMT2A::AFF1 in Fusion Inspector:

But only 2 if they find for gene KMT2A in scout. This is the case:

I believe the problem might be in our parsing of the third variant. Check what you get if you look for the other fusion partner instead (AFF1):

[northwestwitch]

The VCF looks OK:

11    118482495    .    N    N[4:87084120[    .    PASS    SVTYPE=BND;CHRA=11;CHRB=4;GENEA=KMT2A;GENEB=AFF1;POSA=118482495;POSB=87084120;ORIENTATION=+,+;FOUND_DB=COSMIC,Mitelman,FusionGDB2;FOUND_IN=arriba,starfusion,fusioncatcher;TOOL_HITS=3;SCORE=0.688;FRAME_STATUS=INFRAME;TRANSCRIPT_ID_A=ENST00000531904;TRANSCRIPT_ID_B=ENST00000395146;TRANSCRIPT_VERSION_A=6;TRANSCRIPT_VERSION_B=8;HGNC_ID_A=7132;HGNC_ID_B=7135;EXON_NUMBER_A=9;EXON_NUMBER_B=5;ANNOTATIONS=Mitelman,ChimerKB,ChimerPub,Cosmic,ChimerSeq,CCLE_StarF2019,INTERCHROMOSOMAL[11--4]    GT:DV:RV:FFPM    ./1:35:4:0.4128
11    118482092    .    N    N[4:87084120[    .    PASS    SVTYPE=BND;CHRA=11;CHRB=4;GENEA=KMT2A;GENEB=AFF1;POSA=118482092;POSB=87084120;ORIENTATION=+,+;FOUND_DB=COSMIC,Mitelman,FusionGDB2;FOUND_IN=arriba,starfusion,fusioncatcher;TOOL_HITS=3;SCORE=0.688;FRAME_STATUS=FRAMESHIFT;TRANSCRIPT_ID_A=ENST00000531904;TRANSCRIPT_ID_B=ENST00000395146;TRANSCRIPT_VERSION_A=6;TRANSCRIPT_VERSION_B=8;HGNC_ID_A=7132;HGNC_ID_B=7135;EXON_NUMBER_A=8;EXON_NUMBER_B=5;ANNOTATIONS=Mitelman,ChimerKB,ChimerPub,Cosmic,ChimerSeq,CCLE_StarF2019,INTERCHROMOSOMAL[11--4]    GT:DV:RV:FFPM    ./1:3:1:0.0326
11    118482495    .    N    N[4:87084123[    .    PASS    SVTYPE=BND;CHRA=11;CHRB=4;GENEA=KMT2A;GENEB=AFF1;POSA=118482495;POSB=87084123;ORIENTATION=+,+;FOUND_DB=COSMIC,Mitelman,FusionGDB2;FOUND_IN=arriba,starfusion,fusioncatcher;TOOL_HITS=3;SCORE=0.688;FRAME_STATUS=INFRAME;TRANSCRIPT_ID_A=ENST00000531904;TRANSCRIPT_ID_B=ENST00000395146;TRANSCRIPT_VERSION_A=6;TRANSCRIPT_VERSION_B=8;HGNC_ID_A=7132;HGNC_ID_B=7135;EXON_NUMBER_A=9;EXON_NUMBER_B=5;ANNOTATIONS=Mitelman,ChimerKB,ChimerPub,Cosmic,ChimerSeq,CCLE_StarF2019,INTERCHROMOSOMAL[11--4]    GT:DV:RV:FFPM    ./1:2:2:0.0224

[northwestwitch]

Inspecting the VCF I found this variant, which is also mapping to the exact coordinates of the missing variant, the one with gene KMT2A:

11 118482495 . N N[4:87084120[ . PASS SVTYPE=BND;CHRA=11;CHRB=4;GENEA=AP001267.5;GENEB=AFF1;POSA=118482495;POSB=87084120;ORIENTATION=nan,nan;FOUND_DB=nan;FOUND_IN=arriba,fusioncatcher;TOOL_HITS=2;SCORE=0.125;FRAME_STATUS=nan;TRANSCRIPT_ID_A=nan;TRANSCRIPT_ID_B=nan;TRANSCRIPT_VERSION_A=0;TRANSCRIPT_VERSION_B=0;HGNC_ID_A=0;HGNC_ID_B=7135;EXON_NUMBER_A=0;EXON_NUMBER_B=0;ANNOTATIONS=nan GT:DV:RV:FFPM ./1:0:0:0.0

Since this variant with gene A AP001267.5 instead of KMT2A occurs before in the VCF, it gets loaded instead of the latter because of how scout works (same problem as the variant in CALR gene loaded only once if found in SNVs and SVs). So it's not really a bug but a design thing (or limitation), I guess.

Of course one might argue that this is not the intended behaviour. I'm not really sure how to fix this. 🤔