- Integration of Mutect2 (GATK4) for tumorOnly and Panel variant calling
- Analysis of the TSO500 panel including DNA and RNA parts of the panel
- Calcualtion of various complex biomarkers like TMB, MSI, HRD, etc.
- Calcualtion of more QC metrics, e.g. bioinformatic tumor cell content (purity)
- Various bugfixes
- Adjustments of the PDF report mainly structure and readability
- Updated ClinVar version to clinvar_20210123
- Introduced duplicate removal for panel pipeline
- Implemented advanced qc and coverage metrics
- Included RNA Fusion detection for panels containing RNA data
- Update of several annovar databases; re-start of ./setup.sh -t setup_tools recommended.
- Interation of a "tumorOnly" Pipeline
- Implementation of a tNGS Pipeline
- minor bugfixes
- MIRACUM-Pipe extended to tNGS (tested with Illumina TruSight Tumor 170 panel)
- gnomAD database updated to gnomAD_genome v2.1.1
- UCSC SQL server is now used to annotate CNV regions per default
- Report extended and revised to include links to genome nexus and The Variant Interpretation for Cancer Consortium Meta-Knowledgebase
- stability improvments
- various bugfixes
- Added export of variants and copy number alterations for later import into cBioPortal
- Removed automatic OncoKB file download due to licence
- How-to help to get cancerGeneList.tsv and oncokb_biomarker_drug_associations.tsv from OncoKB after registration
- Initial release of MIRACUM-Pipe-docker v1.0.0