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End-to-end examples (GATK 4.6)

Prerequisites

Installation, reference bundles, and all dependencies must be completed beforehand.

➡️ Installation

This example demonstrates how to run CBIcall on a real WES sample from FASTQ files through final VCF and QC outputs.

1. Prepare your FASTQ files

CBIcall expects paired-end FASTQ files with a shared prefix, for example:

# Project    / Sample (Proband WES)
CNAG999_exome/CNAG99901P_ex/
  CNAG99901P_ex_S1_L001_R1_001.fastq.gz
  CNAG99901P_ex_S1_L001_R2_001.fastq.gz

Note on nomenclature

Please see this page.

2. Create a parameters file

Create a YAML file, e.g. wes_single.yaml:

mode:            single
pipeline:        wes
workflow_engine: bash
gatk_version:    gatk-4.6
sample:          CNAG999_exome/CNAG99901P_ex
genome:          b37
cleanup_bam:     false

Notes:

  • mode selects single-sample or cohort (joint genotyping).
  • pipeline switches between WES, WGS or mtDNA.
  • workflow_engine chooses the backend (bash or snakemake).

3. Run CBIcall

bin/cbicall -p wes_single.yaml -t 4
  • -p selects the YAML parameters file
  • -t sets the number of threads

4. Inspect outputs

After completion, you will find:

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

Where:

  • VCF files are stored in 02_varcall/
  • QC metrics (coverage, sample stats, sex prediction) are in 03_stats
  • Logs for all pipeline steps are under logs/

These files are ready for downstream analysis, annotation or integration with cohort-level studies.

For advanced parameters, multi-sample analyses, mtDNA workflows and troubleshooting, see the Usage and FAQ sections.

Important

In order to run a cohort based calculation you first have to create GVCF for each sample. This is being done by running wes mode single.

1. Create a sample map file like the one we display below:

CNAG99901P_ex   /media/mrueda/2TBS/CNAG/Project_CBI_Call/cbicall/examples/input/CNAG999_exome/CNAG99901P_ex/ref_cbicall_bash_wes_single_b37_gatk-4.6_765963065360466/02_varcall/CNAG99901P.hc.QC.vcf.gz
CNAG99902P_ex   /media/mrueda/2TBS/CNAG/Project_CBI_Call/cbicall/examples/input/CNAG999_exome/CNAG99901P_ex/ref_cbicall_bash_wes_single_b37_gatk-4.6_765963065360466/02_varcall/CNAG99901P.hc.QC.vcf.gz

GATK needs absolute paths for the files.

2. Create a parameters file

Create a YAML file, e.g. wes_cohort.yaml:

mode:            cohort
pipeline:        wes
workflow_engine: bash
gatk_version:    gatk-4.6
genome:          b37
sample_map:      ./sample_map.tsv

3. Run CBIcall

bin/cbicall -p wes_cohort.yaml -t 4
  • -p selects the YAML parameters file
  • -t sets the number of threads

4. Inspect outputs

After completion, you will find:

cbicall_bash_wes_cohort_gatk-4.6_*/
  02_varcall/
  logs/

Where:

  • Final VCF files are stored in 02_varcall/
  • Logs for all pipeline steps are under logs/