> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/how_do_i_analyze_mtdna_variants.md).

# How do I analyze mtDNA variants?

To run mtDNA variant analysis on Emedgene, you need to upload:

a. FASTQ files, or

b. VCF file(s) created with [DRAGEN](https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html) / [mity](https://github.com/KCCG/mity) / [MuTect](https://software.broadinstitute.org/cancer/cga/mutect) / [CNVkit](https://cnvkit.readthedocs.io/en/stable/) using the [rCRS](https://www.mitomap.org/MITOMAP/HumanMitoSeq) mtDNA genome reference or a full genome reference that includes rCRS (e.g., hs37d5).

In case of an end-to-end analysis starting from FASTQ files, mtDNA SNV/indel variants will be mapped to rCRS and called by DRAGEN with improved variant quality calculation.


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