Update changelog for next version

CHANGELOG.md

@@ -1,5 +1,19 @@
 # Change Log
 
+## v0.11.0 - 2024-04-18
+
+Improve a number of discovery and scoring features related to inversions, inverted breakpoints and large deletions.
+
+### Changed
+- CR-323 Improve scoring for a number of cases relevant to inversions and inverted breakpoints
+- CR-321 Change contig flank size handling to improve large inversion calling
+- CR-318 Expand trimmed read search region for large SV candidates
+  - Improves recall for inverted breakpoints and duplications
+- CR-317 Standardize on csi indexing for bam output
+
+### Fixed
+- CR-324 Fix non-deterministic inversion output
+
 ## v0.10.0 - 2024-03-05
 
 Initial github release

docs/user_guide.md

@@ -105,6 +105,7 @@ All phred-scaled quality scores in the VCF output have a maximum value of 999.
 
 The following filters may be applied to each VCF record:
 
+- `ConflictingBreakpointGT` - Genotypes of breakpoints in a multi-breakpoint event conflict in the majority of cases (This filter is only relevant to inversions at present)
 - `MinQUAL` - The SV allele quality score (`QUAL`) is less than 10
 - `MaxScoringDepth` - Read depth at the SV locus exceeds 1000x, so all scoring and genotyping steps were disabled.
 - `InvBreakpoint` - This breakpoint is represented as part of a separate VCF inversion record (the inversion record shares the same EVENT ID)