# 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.