Quickstart¶

This page is the shortest path to a validated local test run using the example data shipped in the repository.

If you first need to decide which installation method or workflow applies to you, start with Choose your path.

1. Confirm the CLI is available¶

You can check the command-line interface using:

bin/cbicall --help

To display the version:

bin/cbicall --version

2. Run the shipped WES smoke test¶

This is the most reliable first run because it uses the same example layout used by the integration test script.

cd examples/input
./run_tests.sh --wes

What this does:

runs cbicall on the bundled WES example
compares the resulting VCF against the shipped reference output
exits non-zero if the result differs

When the test completes successfully, you should have a run directory like:

CNAG999_exome/CNAG99901P_ex/cbicall_bash_wes_single_b37_gatk-4.6_*/
  01_bam/
  02_varcall/
  03_stats/
  logs/

The final VCF will be located at:

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

3. Run the shipped mtDNA smoke test¶

Run this after the WES example is working. The mtDNA example depends on the WES/WGS-style project structure and uses the bundled mtDNA example configuration.

cd examples/input
./run_tests.sh --mit

When the test completes successfully, you should have a run directory like:

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

Start by checking:

02_browser/README.txt

4. Run CBIcall directly with a YAML file¶

Once the smoke tests work, the minimal direct invocation is:

bin/cbicall -p param.yaml -t 8

-p selects the parameter file
-t sets the number of threads

5. Next steps¶

Use Choose your path if you are still deciding between installation methods or workflows.
For a realistic WES walkthrough, see End-to-end example WES.
For mtDNA, see End-to-end example mtDNA.

➡️ End-to-end example WES