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Frequently Asked Questions

WES / WGS​

What reference genomes are used?

CBIcall supports:

  • GRCh37 / b37: GATK-compatible reference genome
  • GRCh38 / hg38: GATK-compatible reference genome
What capture kits are used for WES?
  • GATK 3.5: exome capture is based on Agilent SureSelect.
  • GATK 4.6: exome and WGS references are based on the GATK bundle.

mtDNA (MToolBox)​

What reference genome is used?

mtDNA workflows use RSRS (rsrs), the Reconstructed Sapiens Reference Sequence.

VCF vs. prioritized variants allele notation
note

In rare cases, the allele reported in prioritized_variants.txt may differ from the ALT allele reported in the VCF.

The Variant_Allele column is generated during annotation and prioritization and does not always follow VCF semantics, where ALT is defined relative to the mapping reference, such as RSRS.

What does GT=1 mean in results?

In variant reports, the Genotype (GT) field shows the observed allele using VCF allele indices:

  • 0 = reference allele
  • 1 = first alternate allele
  • 2, 3, ... = additional alternate alleles in multiallelic records

For CBIcall mtDNA reports, GT=1 means an ALT allele was detected in that sample.

Biological interpretation should use:

  • HF: heteroplasmy fraction, or molecules supporting ALT
  • DP: read depth, or total support
tip

For mtDNA, GT tells you which allele was detected, not how much of it was detected. Use HF and DP to interpret heteroplasmy or homoplasmy.

General​

How do I set up cbicall on an HPC system?

On most HPC systems, Docker is not available. CBIcall is designed to run with Apptainer, formerly Singularity, which is the recommended approach for HPC environments.

Apptainer can execute Docker images directly, requires no root privileges, and integrates cleanly with batch schedulers.

In this setup:

  • the container image is read-only
  • configuration files and workflows are stored in a writable host directory
  • external databases are downloaded outside the container and bind-mounted at runtime

Recommended workflow:

  1. Pull the CBIcall container image using Apptainer.
  2. Download the required databases on the host filesystem.
  3. Create a writable copy of the CBIcall workflow directory.
  4. Run the pipeline by bind-mounting the writable copy and data directory.

See HPC with Apptainer / Singularity.

Do you have a Slurm + Apptainer example?

Yes. See the example script:

run_cbicall_apptainer_slurm.sh

How do I cite CBIcall?

Please cite:

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. Preprint DOI.