pairing subpackage

Sub-package Documentation

This is the package responsible for pairing/grouping calls between libraries. In many cases this will be where somatic vs germline is determined or genomic only vs expressed.

Output Files

expected name/suffix

file type/format




call information and pairing information using product id

Algorithm Overview

  • pairwise comparison of breakpoint pairs between libraries

    • fail if orientations do not match

    • fail if template/chromosomes do not match

    • if the protocols are mixed

      • pass if the fusion products match at the sequence level

      • pass if the breakpoint predicted from the genome matches the transcriptome breakpoint

    • if the protocols are the same

      • pass if the breakpoints are co-located

  • filter matches based on annotations

    • if both breakpoints have the same gene annotation, they must also both have the same transcript annotation