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	content
mavis_paired_*.tab	text/tabbed	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

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modules

• constants module
• main module
• pairing module