Interpreting Fusions Variants in VCFs: A Handy Tool

         August 22, 2023

When interpreting fusions in their VCF format, it is not easy immediately grasp which side of the positions are adjacent in the resulting fusion. When interpreting and troubleshooting fusion variants, I usually find myself reaching for the VCF spec. If you, like me, are looking to speed up this process and gain a quick understanding of the fusions in your VCF file and the resulting mutation, here is a small tool to visualize them:

Feel free to try lines from one of your own vcf files. Just copy the line from the beginning through the ALT field. If you don’t have a fusion VCF handy, here are a couple of examples you can try from the VCF specification.

  • 2 321681 bnd_W G G]17:198982]
  • 2 321682 bnd_V T ]13:123456]T
  • 13 123456 bnd_U C C[2:321682[
  • 13 123457 bnd_X A [17:198983[A
  • 17 198982 bnd_Y A A]2:321681]
  • 17 198983 bnd_Z C [13:123457[C

You will notice that each fusion pair contains two lines in the VCF; however, each line has enough information to construct the resulting fusion. For example, “2 321682 bnd_V T ]13:123456]T” describes the same fusion as “13 123456 bnd_U C C[2:321682[” just from the other end, you will note though that the image for these fusions doesn’t change.

Fusion image representing "2 321682 bnd V T ]13:123456]T"

Describing the call from both ends of the fusion allows for specifying additional information, such as the supporting reads and wild-type reads at each end. To learn more about fusions and how they are imported and represented into VarSeq, check out this blog post. If you have any further questions feel free to reach out to

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