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CBIcall

CBIcall
Reproducible germline variant calling for WES, WGS, and mtDNA

What is CBIcall?

CBIcall (CNAG Biomedical Informatics framework for variant calling) is a lightweight, reproducible germline variant-calling framework developed at CNAG.
It wraps established best practices (BWA → GATK → VQSR or hard filters) into easy-to-run Bash and Snakemake workflows, enabling labs to produce high-quality single-sample and cohort VCFs with minimal effort. 🧬

Why CBIcall?

  • Implements GATK best practices (GATK 4.6 and GATK 3.5 legacy modes), tuned for real project needs.
  • Supports both single-sample and cohort pipelines (WES and WGS), using GenomicsDBImport or per-chromosome sharding.
  • Includes robust mitochondrial DNA analysis via MToolBox with heteroplasmy-aware calling.
  • Simple YAML configuration with sensible defaults for fast onboarding.
  • Transparent logs and structured outputs suitable for QC, auditing, and downstream interpretation.

Key features

  • Per-sample preprocessing: alignment, read groups, merging, duplicates, and BQSR.
  • High-quality variant calling: per-sample gVCFs and scalable joint genotyping.
  • Variant quality control: VQSR when possible, with reproducible hard-filter fallback.
  • mtDNA pipelines: MToolBox-based assembly, annotation, and heteroplasmy estimation.
  • Flexible deployment: Bash and Snakemake workflows; supports containerized environments.
  • Utility tools: coverage estimation, sex determination, basic cohort QC metrics.

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