bio-clinical-databases-tumor-mutational-burden

You compute tumor mutational burden by providing a somatic VCF path and a panel name to apply panel-aware normalization, variant filtering, and annotation checks to output clinically actionable TMB scores.

Panel-aware normalization adjusts tumor mutational burden calculations by referencing panel sizes for targeted sequencing data like FoundationOne or MSK-IMPACT, ensuring accurate TMB scores for immunotherapy decisions.

Yes, the TMB calculation supports both panel-based sequencing data like FoundationOne and MSK-IMPACT, as well as whole-exome sequencing, applying appropriate normalization and variant filtering for each data type.

Yes, you can batch process multiple somatic VCFs across cohorts to compute TMB and export the results into summary tables for downstream immunotherapy decision-making.

The calculation references standard annotation formats like VEP or SnpEff during variant filtering and uses cyvcf2 for VCF parsing to accurately compute tumor mutational burden from your data.

FDA-like thresholds are applied to classify the normalized tumor mutational burden scores, providing clinical context to support immunotherapy decision-making and optional MSI comparison.