pandora container doc

src/pipes/somatic.rs

@@ -1,3 +1,63 @@
+//! # SomaticPipe
+//!
+//! End-to-end somatic variant calling and annotation pipeline.
+//!
+//! `SomaticPipe` orchestrates the complete workflow for detecting,
+//! filtering, annotating, merging, and exporting high-confidence
+//! somatic variants from paired tumor/normal sequencing data.
+//!
+//! ## Main Features
+//!
+//! - Multi-caller somatic variant integration
+//! - Germline and constitutional filtering
+//! - BAM depth and allele support annotation
+//! - Sequence complexity and entropy filtering
+//! - External annotation (COSMIC, GnomAD, VEP)
+//! - Structural insertion annotation via NanomonSV
+//! - Export to JSON, VCF, BIT, and Pandora container formats
+//! - Detailed QC and filtering statistics
+//!
+//! ## Supported Variant Callers
+//!
+//! - ClairS
+//! - DeepSomatic
+//! - DeepVariant
+//! - NanomonSV
+//! - SAVANA
+//! - Severus
+//!
+//! ## Pipeline Overview
+//!
+//! 1. Initialize prerequisite components
+//! 2. Load somatic and germline variants
+//! 3. Remove germline/constitutional calls
+//! 4. Annotate constitutional BAM support
+//! 5. Filter low-depth and high-alt variants
+//! 6. Annotate sequence context and entropy
+//! 7. Annotate external databases (COSMIC/GnomAD)
+//! 8. Filter likely polymorphisms
+//! 9. Annotate VEP consequences
+//! 10. Merge and export final variants
+//!
+//! ## Outputs
+//!
+//! - `*_somatic_variants.json.gz`
+//! - `*_somatic_variants.bit`
+//! - `*_somatic_variants.vcf.gz`
+//! - `*.pandora`
+//! - QC/statistics JSON reports
+//!
+//! ## Notes
+//!
+//! The pipeline conditionally executes missing upstream analyses
+//! and tracks filtering statistics throughout processing.
+//!
+//! This module also defines:
+//!
+//! - [`SomaticPipeStats`]
+//! - [`InputStats`]
+//! - Pandora export helpers
+//! - Annotation matrix generation utilities
 use crate::{
     annotation::{is_gnomad_and_constit_alt, Caller},
     create_should_run_normal_tumoral, init_solo_callers_normal_tumoral,