Included Pipelines

CBIcall ships curated variant-calling pipelines for Illumina DNA sequencing. These are the analyses available out of the box.

Included pipeline	Modes	Main output
WES	Single-sample and cohort joint genotyping	Germline VCF/gVCF outputs for exome data
WGS	Single-sample and cohort joint genotyping	Germline VCF/gVCF outputs for genome data
mtDNA	Single-sample and cohort/family analysis	mtDNA VCF, prioritized variant table, and browser report

The selected pipeline is configured with pipeline and mode:

pipeline: wes
mode: single

The workflow backend is configured separately with workflow_backend. See Native Backends for Bash, Snakemake, Nextflow, Cromwell, and external nf-core execution.

Pipeline Guides

Goal	Page
Process one WES/WGS sample from FASTQ	WES/WGS Single-Sample
Joint-genotype a WES/WGS cohort from gVCFs	WES/WGS Cohort
Run mitochondrial variant calling	mtDNA

Backend Availability

Backend coverage differs by pipeline family:

Pipeline	Bash	Snakemake	Nextflow	Cromwell
WES	Yes	Yes	Yes	Single-sample only
WGS	Yes	Yes	Yes	No
mtDNA	Yes	No	No	No

External nf-core workflows are registered through the Nextflow backend, but they are not part of the included WES/WGS/mtDNA pipeline set.