- Introduced boundary distance comparison to replace reciprocal overlap in wit.ty
- --percentageDistance (-pd) and --basepairDistance (-bpd) are introduced to replace -po and -bpo
- For intra-chromosome breakend pair, distance between the pair is used in boundary distance comparison, see breakend comparison
- Breakend is now binned based on distance between the pair, inter-chromosome breakend always fall into the last bin
- Insertion is now using the same strategy as breakend comparison, basepair distance can be tuned through -bpd (hardcoded to be 200bp in wit.ty)
- --simpleCounting (--sc) and --crossTypeMatching (--ct) options are now merged into one option --evaluationMode with accepted values to be Default(d) , SimpleCounting(sc), CrossTypeAndSimpleCounting(cts)
- Base level stats is fully supported for DEL, DUP and CNV
- New and improved set of vcf annotation, see vcf annotation
- Support vcf output from WGSv8, TNWv6 and latest DragenCNV
- Inserted sequence is not used in Insertion evaluation
- Limited support for multi-allelic entries
- Multi-alts with different SVTYPEs are annotated as NotAssessed(N) and completely left out from stats
- For multi-alt CNV gains, witty.er currently only using total CN for evalutation disregard CN number of individual ALT.