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Quickstart

This page provides a minimal introduction to using CBIcall.
It focuses on basic commands, help options, and a simple built-in test run.

1. Basic usage

You can check the command-line interface using:

bin/cbicall --help

To display the version:

bin/cbicall --version

2. Minimal command example

Once you have a parameters file (YAML), you can run:

bin/cbicall -p param.yaml -t 8
  • -p selects the param file
  • -t sets the number of threads

This is the minimal invocation required for any workflow.

3. Run a small WES job (workstation)

CBIcall includes small test configurations to validate that your installation works.

Example:

cd examples/input
../../bin/cbicall -p wes_single.yaml -t 4

When the job completes successfully (<2 min), you should see:

CNAG999_exome/CNAG99901P_ex/cbicall_bash_wes_single_gatk-4.6_*/
  01_bam/
  02_varcall/
  03_stats/
  logs/
The final VCF will be located at:

02_varcall/CNAG99901P.hc.QC.vcf.gz

4. Run a small mtDNA job (workstation)

Example:

cd examples/input # ommit if you are already there
../../bin/cbicall -p mit_single.yaml -t 4

When the job completes successfully (~ 5 min), you should see:

CNAG999_exome/CNAG99901P_ex/cbicall_bash_mit_single_gatk-3.5_*/
  01_mtoolbox/
  02_browser/

We recommend you to check:

02_browser/README.txt

5. Next steps

For a complete, real-case workflow demonstration, see:

➡️ End-to-end example WES