gatk
gatk copied to clipboard
Complex SV intervals support
- Complex (CPX) SV records no longer use
END2
/CHR2
INFO fields and instead are defined byCPX_INTERVALS
in addition to normal coordinates. - Adds new class
SVCallRecord.ComplexEventInterval
for storing complex event intervals, which are associated with a particular SV type. - SV clustering now takes into account CPX subtype and intervals, requiring intervals to match on type and interval similarity as defined by the clustering parameters (e.g. minimum reciprocal overlap).
- Improved reciprocal translocation (CTX) record handling. In particular, these records are now treated similarly to BNDs for clustering purposes.
- Added unit tests for new CPX cases.