vcffuse

Visualising gene fusions in VCFs

The main purpose is to visualise structural variants in a similar way like in this article.

Features

Presently it is restricted to file format generated by Manta and annotated by snpEff . Goal is to follow structural variants as they are described in the VCF Specification

• TODO

  • generally refactor code, actual steps below
  • add test cases
  • refactor all the functions that are ad-hoc added to code
  • check tandem repeats https://github.com/szilvajuhos/vcffuse/blob/master/vcffuse/getFusionFromVCF.py#L198

  • DRY in

    • fuse_deletion()
    • fuse_tandem_genes()
    • fuse_translocations()

• Usage:

It is not a module yet, add a conda environment stored in environment.yml and try

$ python vcffuse/getFusionFromVCF.py