rRNA hotspots

Coded needed to generate figures seen in main text and extended data.

Directory structure

    ├── 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

For SNV hotspot mutations run

./src/GEL/run_snv_hotspots.R

Ensure you have the following files:

• mtDNA MAF file with the following fields
  • flanking_bps = the flanking nucleotides
  • pos = genomic position
• Annotated genome .fa file
• Annotated chrM (see Supplementary Table 5)