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Choose Your Path

Use this page to decide which installation route and workflow to run before diving into the detailed documentation.

1. Choose how you will run CBIcall

Use Docker if:

  • You are on a local Linux workstation or server.
  • You want the fastest setup.
  • You do not need an HPC scheduler integration.

Go to Docker installation.

Use Apptainer if:

  • You are on an HPC cluster.
  • Docker is not available.
  • You need a container workflow that works with batch schedulers.

Go to Apptainer installation.

Use the non-containerized setup if:

  • You want to inspect or modify the source tree directly.
  • You already manage Python and Java on the host.
  • You are developing or debugging workflows.

Go to Non-containerized installation.

2. Choose the analysis you want to run

Run wes if:

  • Your input data is whole-exome sequencing.
  • You want standard germline calling for one sample or a cohort.

See WES/WGS single-sample pipeline and WES/WGS cohort pipeline.

Run wgs if:

  • Your input data is whole-genome sequencing.
  • You want the same general calling flow as WES, but genome-wide.

See WES/WGS single-sample pipeline and WES/WGS cohort pipeline.

Run mit if:

  • You want mtDNA calling with MToolBox.
  • You already have BAM output from a previous WES/WGS single-sample run.

Important: mtDNA mode does not start from FASTQ in this project documentation flow.

See mtDNA pipelines and End-to-end example (mtDNA).

3. Choose single or cohort

Use single if:

  • You are processing one individual.
  • You need a per-sample VCF or gVCF.
  • You are preparing inputs for a later cohort run.

Use cohort if:

  • You want joint genotyping across multiple samples.
  • You already have the required per-sample gVCFs for WES/WGS.
  • For mtDNA, you already have the required WES/WGS BAM outputs for all samples.

4. Choose the workflow engine

Use bash if:

  • You want the most broadly supported option.
  • You are running mtDNA.
  • You want behavior that matches the legacy and example scripts most closely.

Use snakemake if:

  • You want Snakemake orchestration for supported WES/WGS workflows.
  • You are using gatk-4.6.

Important: snakemake is not supported for mit, and it is not supported with gatk-3.5.