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CHANGELOG.md

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Changelog

Release v4.0.1

  • Remove cnvkit parameters section in .yaml
  • Adjusted coverage parameters settings for panel analysis
  • Improved handling of multiple fastq files for tNGS, i.e. multiple fastq files are now concatenate before further processing

Release v4.0.0

  • Integration of Mutect2 (GATK4) for tumorOnly and Panel variant calling
  • Analysis of the TSO500 panel makes us of the DNA and RNA part of the panel
  • Integration of sequenza for HRD calculation
  • Calcualtion of various complex biomarkers like TMB, MSI, HRD
  • Calcualtion of more QC metrics, e.g. bioinformatic tumor cell content (purity)
  • Using predicted ploidy and tumor cell content values from sequenta as input for ControlFREEC
  • Use BAF functionality of ControlFREEC
  • Various bugfixes
  • Adjustments of the PDF report; mainly structure and readability

Release v3.1.0

  • Updated ClinVar version to clinvar_20210123; re-run of ./setup.sh -t setup_tools from the MIRACUM-Pipe-docker repository recommended or manual installation of the updated annovar databases:
# annovar databases
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar clinvar_20210123 humandb/
  • Introduced duplicate removal for panel pipeline
  • Implemented advanced qc and coverage metrics
  • Included RNA Fusion detection for panels containing RNA data

Minor Updates

  • Update of several annovar databases; re-start of ./setup.sh -t setup_tools from the MIRACUM-Pipe-docker repository recommended or manual installation of the updated annovar databases:
# annovar databases
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp41a humandb/
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar clinvar_20200316 humandb/

Release v3.0.0

  • Interation of a "tumorOnly" Pipeline
  • Implementation of a tNGS Pipeline

Release v2.0.1

  • minor bugfixes

Release v2.0.0

  • 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

Release v1.2.0

  • Added export of copy number alterations for later import into cBioPortal

Release v1.1.0

  • Included export into a maf file for later import into cBioPortal

Minor Release v1.0.1

  • Added support for more than 64GB of RAM
  • Included txt2maf function as possible import format into cBioPortal

Release v1.0.0

  • Initial release of MIRACUM-Pipe v1.0.0