# 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.


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/how_do_i_analyze_mtdna_variants.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.