Coded needed to generate figures seen in main text and extended data.
├── data
│ ├── conservation_rate.tsv
│ ├── data_mutations_pcawg.txt
│ ├── data_mutations_tcga.txt
│ ├── helix_mutations.csv
│ ├── hotspots_snv_1.txt
│ ├── hotspots_snv_5.txt
│ ├── hotspots_snv_pcawg.txt
│ ├── hotspots_snv_precalculated.txt
│ ├── indels_snp_1.txt
│ ├── indels_snp_5.txt
│ ├── maf_snp_1.txt
│ ├── maf_snp_5.txt
│ └── mito_rRNA_annotations_NL.tsv
├── results
│ ├── 143b
│ └── hek293
├── README.md
└── src
├── 143b
├── GEL
├── hek293
└── prerequisites.R
For code to call mtDNA variants, please refer to https://github.com/sboscenco/mtdna-vc
./src/GEL/run_snv_hotspots.R
Ensure you have the following files:
- mtDNA MAF file with the following fields
flanking_bps= the flanking nucleotidespos= genomic position
- Annotated genome .fa file
- Annotated chrM (see Supplementary Table 5)