diff --git a/CHANGELOG.md b/CHANGELOG.md index 293bf77..54a705a 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/docs/user_guide.md b/docs/user_guide.md index f4243ac..9898642 100644 --- a/docs/user_guide.md +++ b/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)