Change log

21-06-07

• fixing broken IGV port command links.

21-06-02

• harmonization of parameter nomenclature across all TSOPPI tools (please note: this implies numerous parameter name changes in the tool set);

• introduction of a new parameter to the DNA and RNA post-processing tools: “–inpred_nomenclature” (InPreD sample ID nomenclature will be assumed to be in use only if this parameter is set to “True”);

• when applicable, the new InPreD sample ID nomenclature is now reflected in all sample-wise QC plots;

• changing multiple internal parameter values in the DNA sample post-processing tool (these parameters don’t affect which variants will be present in the output files, they only affect how the output variants will be flagged): MIN_TUMOR_DP: 10 -> 50; MIN_TUMOR_VAF: 0.03 -> 0.05; MAX_TUMOR_VAF: 0.98 -> 0.99;

• changing “*htm” files into “*html” files.

21-05-24

• when utilizing a normal sample, the pipeline version string should now correctly conveys that information (stating “TN”, instead of the previous erroneous “T”);

• genome-wide CNV plots now display centromeres, BAF plots now show GL_P variants;

• instead of the number of processed samples, the variant recurrence strings now show the number of callable samples for given variant position.

21-04-14

• initial version.