skills/bioskills/bio-clinical-databases-tumor-mutational-burden/scripts/tmb_calculation.py

• is_target_variant · function · L55-L70 — def is_target_variant(variant, include_synonymous=False, csq_header_consequence_idx=1)
• get_vaf · function · L73-L89 — def get_vaf(variant)
• calculate_tmb · function · L92-L153 — def calculate_tmb(vcf_path, assay='foundationone_cdx', min_vaf=0.05, min_depth=100, max_gnomad_grpmax_faf95=0.005, exclude_hotspots=False, hotspots_bed=None)
• classify_tmb_tier · function · L156-L169 — def classify_tmb_tier(tmb, cutoff=10.0)
• tmb_msi_decision · function · L172-L193 — def tmb_msi_decision(tmb_value, msi_status, tumor_type=None, hla_loh=False)