Calculate-mtDNA-CopyNumber

• Calculate-mtDNA-CopyNumber
  • Overview
  • How To Run
  • Inputs
  • Outputs
  • References
  • Discussions
  • Contributors
  • License

Overview

Calculate-mtDNA-CopyNumber estimates mitochondrial DNA copy number using autosomal and mitochondrial coverages modified by ploidy:

$$mtDNA\ CopyNumber = \frac{mtDNA\ average\ coverage}{autosomal\ DNA\ average\ coverage} \cdot ploidy$$

The pipeline takes as input contig-stratified coverage information and calculates the mtDNA copy number for each source of coverage provided.

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How To Run

1. Copy and edit the input config file

2. Copy and edit the input YAML

3. The pipeline can be executed locally using the command below:

nextflow run path/to/main.nf -c path/to/input.config -params-file path/to/input.yaml

4. To submit to UCLAHS-CDS infrastructure, use the submission script here

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Inputs

Input YAML

sample_id: 'sample_id'
input:
  coverage:
    Qualimap: '/path/to/qualimap/coverage'

Config

Field	Type	Required	Description
output_dir	path	yes	Path to which outputs should be saved.
work_dir	path	no	Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With ucla_cds, the default is /scratch and should only be changed for testing/development. Changing this directory to /hot or /tmp can lead to high server latency and potential disk space limitations, respectively.

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Outputs

Output	Description
mtDNA-copynumbers.txt	List of calculated mtDNA copy numbers organized by coverage source.

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References

1. Ding J, Sidore C, Butler TJ, Wing MK, Qian Y, Meirelles O, Busonero F, Tsoi LC, Maschio A, Angius A, Kang HM, Nagaraja R, Cucca F, Abecasis GR, Schlessinger D. Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools. PLoS Genet. 2015 Jul 14;11(7):e1005306. doi: 10.1371/journal.pgen.1005306. Erratum in: PLoS Genet. 2015 Sep 29;11(9):e1005549. doi: 10.1371/journal.pgen.1005549. PMID: 26172475; PMCID: PMC4501845.

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Discussions

• Issue tracker to report errors and enhancement ideas.
• Discussions can take place in calculate-mtDNA-CopyNumber Discussions
• calculate-mtDNA-CopyNumber pull requests are also open for discussion

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Contributors

Please see list of Contributors at GitHub.

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License

pipeline-calculate-mtDNA-CopyNumber is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.

pipeline-calculate-mtDNA-CopyNumber calculates the mitochondrial DNA copy number based on coverage.

Copyright (C) 2025 University of California Los Angeles ("Boutros Lab") All rights reserved.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.