mtDNA pipelines

The bundled cbicall-core mtDNA workflows extract mitochondrial reads from completed bundled Bash WES/WGS BAMs and use MToolBox to call, annotate, and prioritize mtDNA variants. They do not start from FASTQ files.

Mode	Use
single	Analyze one individual.
cohort	Analyze all eligible samples in one project together.

Architecture

The bundled MToolBox workflow supports x86_64 Linux only.

Single sample

Single-sample workflow

Set input_dir to a sample directory containing a completed bundled Bash WES/WGS single-sample run. CBIcall discovers the recalibrated BAM, extracts the mitochondrial contig, runs MToolBox, and appends genotype (GT), depth (DP), and heteroplasmy fraction values to the prioritized report.

mode:             single
pipeline:         mit
workflow_backend: bash
software_stack:   gatk-3.5
input_dir:        CNAG999_exome/CNAG99901P_ex

Cohort

Cohort workflow

Set input_dir to a project directory containing the sample directories and their completed bundled Bash WES/WGS single-sample runs. CBIcall extracts mitochondrial reads from each usable BAM and runs MToolBox jointly.

mode:             cohort
pipeline:         mit
workflow_backend: bash
software_stack:   gatk-3.5
input_dir:        CNAG999_exome

Use cohort mode for a family, maternal-lineage analysis, or a project-level mtDNA table. A WES/WGS cohort run is not required beforehand.

Outputs

Both modes produce the same principal artifacts:

File	Description
01_mtoolbox/mit_prioritized_variants.txt	Annotated variants with CBIcall-added GT, DP, and heteroplasmy values.
01_mtoolbox/VCF_file.vcf	mtDNA VCF from MToolBox.
01_mtoolbox/mt_classification_best_results.csv	Predicted mitochondrial haplogroups.
01_mtoolbox/mit.filtered.json	Canonical filtered records used to generate the browser.
02_browser/<run-id>.html	Standalone interactive mtDNA report.

See the mtDNA end-to-end example for the complete run procedure and browser screenshots.

Implementation details and source files

The workflow builds on MToolBox v1.0. It converts and prepares the input BAM, aligns mitochondrial reads to RSRS, calls variants, predicts haplogroups, and performs functional annotation and prioritization. CBIcall then creates the canonical filtered JSON and standalone browser report.

• Single-sample Bash workflow
• Cohort Bash workflow
• Calabrese C. et al. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics (2014). Article