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