Fusion orientation make sense or not

Question

[9521ljh]

I use TCGA data and run Structural Variant calling tools(e.g. Delly,Manta...)

Then i annotate the SV breakpoint and pick up fusion gene which met different genes.

ex)

• SV calling output and pick up meeting different genes

  • GeneA--GeneA, 5to5

  • GeneA--GeneC, 3to5 (pick up)

  • GeneB--GeneB, 3to3

  • GeneB--GeneC, 5to3 (pick up)

  • ................

-

• and using GTF file, i add some strand of genes.

  • GeneA(strand: +) -- GeneC(strand: -), 3to5

  • GeneB(strand: +) -- GeneC(strand: +), 5to3

  • GeneC(strand: +) -- Gene Y(strand: -), 5to5

At this point, i'm want to know these gene fusions can be operated. Thus, i consider gene fusion all posible orientation and write it below. However i am not sure my thinking is right, Thus i'd appreciate it if you could check it out and advise me. Thank you

fusion orientation link

Answer 1

[trausch]

I think snpEff can annotate SVs from Delly and Manta in VCF format for potential gene fusions.

Answer 2

[hellosearchorg]

Autodesk has an in-depth explanation of this.

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