How does the data look like between different modules?

How does the data look like between different modules?

Input -A> SV detection -B> clustering -C> refinement -D> Output

A:

• SAM file + fasta

B:

• vector of junctions
  • junctions: 2 breakends + read name
  • breakend: seq_name (chromosome/ref_name) ???, position, orientation (forward/reverse), seq_type (reference/read)

C:

• vector of clusters
  • cluster: breakpoint range?, supporting reads (multiple junctions)

D:

• VCF

Where do we put the interpretation?

Input -A> SV detection -B> clustering -C> refinement -??> Interpretation -D> Output