├── .gitattributes ├── .gitignore ├── Dockerfile ├── Dockerfile.dev ├── LICENSE.txt ├── README.md ├── docs ├── INSTALL.md ├── README.developer.md ├── change_log.md ├── commands.md ├── custom_report_configs.md ├── future_improvements.md ├── mity_report_custom_annotations.md ├── mity_report_documentation.md ├── test_commands.md └── test_files.md ├── mitylib ├── __init__.py ├── _version.py ├── annot_chrm │ ├── chrm_anticodon_positions.bed.gz │ ├── chrm_anticodon_positions.bed.gz.tbi │ ├── chrm_gtf_annotations.bed.gz │ ├── chrm_gtf_annotations.bed.gz.tbi │ ├── chrm_haplotype_data.vcf.gz │ ├── chrm_haplotype_data.vcf.gz.tbi │ ├── chrm_mgrb_variants.vcf.gz │ ├── chrm_mgrb_variants.vcf.gz.tbi │ ├── chrm_mito_dna_func_loc.bed.gz │ ├── chrm_mito_dna_func_loc.bed.gz.tbi │ ├── chrm_mitomap_confirmed_mutations.vcf.gz │ ├── chrm_mitomap_confirmed_mutations.vcf.gz.tbi │ ├── chrm_mitomap_disease.vcf.gz │ ├── chrm_mitomap_disease.vcf.gz.tbi │ ├── chrm_mitomap_mutations_coding_control.vcf.gz │ ├── chrm_mitomap_mutations_coding_control.vcf.gz.tbi │ ├── chrm_mitomap_mutations_rna.vcf.gz │ ├── chrm_mitomap_mutations_rna.vcf.gz.tbi │ ├── chrm_mitomap_polymorphisms.vcf.gz │ ├── chrm_mitomap_polymorphisms.vcf.gz.tbi │ ├── chrm_mitomap_variants_coding.vcf.gz │ ├── chrm_mitomap_variants_coding.vcf.gz.tbi │ ├── chrm_mitomap_variants_control.vcf.gz │ ├── chrm_mitomap_variants_control.vcf.gz.tbi │ ├── chrm_mitotip_scores.vcf.gz │ └── chrm_mitotip_scores.vcf.gz.tbi ├── annot_mt │ ├── anticodon_positions.bed.gz │ ├── anticodon_positions.bed.gz.tbi │ ├── gtf_annotations.bed.gz │ ├── gtf_annotations.bed.gz.tbi │ ├── haplotype_data.vcf.gz │ ├── haplotype_data.vcf.gz.tbi │ ├── mgrb_variants.vcf.gz │ ├── mgrb_variants.vcf.gz.tbi │ ├── mito_dna_func_loc.bed.gz │ ├── mito_dna_func_loc.bed.gz.tbi │ ├── mitomap_confirmed_mutations.vcf.gz │ ├── mitomap_confirmed_mutations.vcf.gz.tbi │ ├── mitomap_disease.vcf.gz │ ├── mitomap_disease.vcf.gz.tbi │ ├── mitomap_mutations_coding_control.vcf.gz │ ├── mitomap_mutations_coding_control.vcf.gz.tbi │ ├── mitomap_mutations_rna.vcf.gz │ ├── mitomap_mutations_rna.vcf.gz.tbi │ ├── mitomap_polymorphisms.vcf.gz │ ├── mitomap_polymorphisms.vcf.gz.tbi │ ├── mitomap_variants_coding.vcf.gz │ ├── mitomap_variants_coding.vcf.gz.tbi │ ├── mitomap_variants_control.vcf.gz │ ├── mitomap_variants_control.vcf.gz.tbi │ ├── mitotip_scores.vcf.gz │ └── mitotip_scores.vcf.gz.tbi ├── call.py ├── commands.py ├── config │ ├── report-config.yaml │ ├── vcfanno-config-chrm.toml │ └── vcfanno-config-mt.toml ├── merge.py ├── mity ├── normalise.py ├── reference │ ├── hg19.chrM.fa │ ├── hg19.chrM.fa.fai │ ├── hg19.dict │ ├── hg19.genome │ ├── hg38.chrM.fa │ ├── hg38.chrM.fa.fai │ ├── hg38.dict │ ├── hg38.genome │ ├── hs37d5.MT.fa │ ├── hs37d5.MT.fa.fai │ ├── hs37d5.dict │ ├── hs37d5.genome │ ├── mm10.MT.fa │ ├── mm10.MT.fa.fai │ ├── mm10.chrM.fa │ ├── mm10.chrM.fa.fai │ └── mm10.genome ├── report.py └── util.py ├── pipeline ├── azure-pipelines-dev.yml ├── 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