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Welcome to the fusebench wiki!

What We're Thinking of Building

Features

A tool that is capable of:

• Importing results from different fusion callers tools (or can convert the results of a set of tools into a common format)
  • Initial idea: have team members write simple parsers to convert tool output formats to a common standard (most likely BEDPE)
• From the common file format, aggregating results from different tools into a consensus set
  • Initial idea: require some level of minimum overlap between features
  • Handling duplicate or 'synonym' calls might be difficult here
• Augmenting the consensus set with additional information from the RNA-Seq data set or existing tools
  • Initial idea: add gene expression data for candidate fusion partners
  • Initial idea: use Oncofuse?
• Importing information from existing databases
  • Initial idea: start from dump of CIViC, filtered for fusions
  • Initial idea: use ReCount to provide view of how common the fusion junction is in different data sets
• Review interface
  • Some kind of dashboard or web view for 'reviewers' to view evidence associated with particular fusions
• Visualization
  • TBD

NOTE that we will almost certainly not be able to tackle all aspects of this project during HackSeq 2017.

Implementation

• Currently, this repository is set up as an R package. The initial idea was to implement most of the components principally in 'tidyverse'-style R, but this is not a hard requirement (it might not make sense for some parts)

Initial Data Sets

• Small test sets from Chimeraviz
• Synthetic test set containing 9 known fusions (from FusionCatcher)
• AML cell line RNA-Seq data (3x replicates from cell line data)