skills/bioskills/bio-clinical-databases-somatic-signatures/scripts/sigprofiler_analysis.py

• generate_matrix · function · L67-L87 — def generate_matrix(vcf_dir, project, genome='GRCh38', exome=False, bed_file=None)
• extract_de_novo · function · L90-L118 — def extract_de_novo(matrix_path, output_dir, min_sigs=1, max_sigs=12, cosmic_version=3.4)
• refit_to_cosmic · function · L121-L141 — def refit_to_cosmic(matrix_path, output_dir, cosmic_version=3.4)
• interpret_signatures · function · L144-L188 — def interpret_signatures(contribution_file, min_contribution_pct=5.0, is_ffpe=False)
• detect_apobec_subtype · function · L191-L208 — def detect_apobec_subtype(matrix_96)