Germline and somatic changes are reported in HTML format using sequences from tumor and normal samples. "ACMG incidental findings", "germline changes in cancer susceptibility genes", "germline changes in DNA repair genes", "GWAS (Genome-Wide Association Study) variants" and "non-synonymous germline changes" are reported under the Germline Variants. Somatic single nucleotide changes and indels (insertions/deletions) are clinically prioritized under the headings of “somatic changes that may be clinically significant”, “non-synonymous changes in cancer genes”, “other non-synonymous changes” and “non-coding changes” and variants that may be drug targets are reported. Somatic copy number changes are presented with a global figure that visualizes chromosomal copy number segments. Somatic copy number changes at the gene level are presented prioritized under the headings of “biomarker copy number changes”, “matched copy number changes in cancer genes” and “all copy number changes”. In addition, tumor mutational burden, microsatellite instability and mutational signatures are detected and reported. The report can be created for general cancer or cancer specific.