Breaking changes:
- Default VIP report template requires a configuration file, see here.
- metadata.json structure is changed, categoricals need to have a label and a description, INFO fields no longer have a "field" property. example
- All nodes in the decision tree json files need to have a label.
- VIP now uses nanopore as default sequencing platfrom instead on illumina.
What's Changed
- Do not split multiallelic variants in #640
- Replace coverage calculation with mosdepth and use regions file in #644
- Sample sheet HPO validation in #651
- Support filtering incomplete penetrance in sample tree in #642
- Update ClinVar 2024-06-03 to 2024-11-26 in #639
- Update ClinVar resource creation: reduce number of categories and map the rest to Other to improve variant classification
- Update VKGL 2024-04-01 to 2024-07-01 in #639
- Update VKGL resource creation: remove contigs that are not in the reference genome
- Update CAPICE model from v5.1.2-v2 to v5.1.2-v3 in #639
- Update default sv.cutesv.min_support value from 10 to 2 in #647
- Update container dependencies to use Alpine Linux v3.20.3 instead of v3.18.3
- Update container dependencies to use OpenJDK 21 instead of 17 in #638
- Update vcf-decision-tree v4.1.1 to v5.1.2 in #648 and #654
- Update vcf-report v7.0.0 to v7.2.0 in #643
- Update vcf-report-template v6.2.0 to v7.0.6 in #643 and #655
- Updated vip-report-inheritance-matcher v3.1.1 to v3.3.2
- Introduced vcf.report.config parameter to configure vcf.report.template, see here
- Increase vcf_report process memory usage from 4GB to 6GB
- Fix: INFO/STR_STATUS metadata to PER_ALT in #653
- Fix: Travis GitHub pages deploy in #645 and #646
- Implemented HTSJDK tandem repeat workaround for samtools/htsjdk#1718
- Annotate 'old chrom-post-ref-alt' for normalized variants in INFO/OLD_REC
- Replace Illumina with nanopore as default sequencing platform by @bartcharbon in #656
Full Changelog: v7.9.1...v8.0.0
Contributors
bartcharbon