Skip to content

🏠 Introduction

Welcome to the documentation for CBICall

CBICall

CBICall (CNAG Biomedical Informatics framework for variant Calling) is a lightweight, reproducible framework for germline variant calling developed at CNAG. Built for Illumina WES/WGS data, CBICall wraps established best-practices (BWA → GATK → VQSR / hard-filters) into easy-to-run Bash and Snakemake workflows so labs can produce high-quality single-sample and cohort VCFs with minimal fuss. đŸ§Ŧ

Why CBICall?

  • Implements GATK best practices (GATK-4.6 and legacy GATK3.5) tuned for real project needs.
  • Supports both single-sample and cohort pipelines (WES / WGS) with GenomicsDBImport and optional per-chromosome sharding.
  • Handles mitochondrial DNA (mtDNA) analysis through MToolBox integration for heteroplasmy-aware calling and mtDNA-specific processing.
  • Simple YAML configuration and sensible defaults to get you running quickly.
  • Transparent, auditable logs and outputs for QC and downstream analysis.

Key features

  • Per-sample preprocessing: alignment, read groups, merging, duplicate marking, BQSR.
  • Per-sample GVCF generation and scalable joint genotyping (GenomicsDBImport → GenotypeGVCFs).
  • Variant quality control: VQSR when cohort size permits, with reproducible hard-filter fallbacks.
  • mtDNA support: MToolBox-based workflows for mitochondrial assembly, heteroplasmy estimation and annotation.
  • Small-footprint workflows: Bash and Snakemake variants, plus optional containerized deployment.
  • Handy utility scripts: coverage stats, sex determination, basic cohort QC.