| extract_mtDNA_BAMQL |
*OUT2-sorted.bam |
main |
Outputs BAM file with only mitochondrial reads |
| align_mtDNA_MToolBox |
.bam |
main |
Aligned, sorted, mitochondrial reads in BAM format |
| align_mtDNA_MToolBox |
prioritized_variants.txt |
main |
Contains annotation only for prioritized variants for each sample analyzed,sorted by increasing nucleotide variability |
| align_mtDNA_MToolBox |
summary*.txt |
main |
Summary of selected options. Includes predicted haplogroups, total and prioritized variants, coverage of reconstructed genomes, count of homoplasmic and heteroplasmic variants |
| align_mtDNA_MToolBox |
.vcf |
intermediate |
Contains mitochondrial variant positions against reference genome |
| align_mtDNA_MToolBox |
.csv |
intermediate |
Contains the best haplogroup prediction for each sequence |
| align_mtDNA_MToolBox |
folder OUT_* |
intermediate |
This folder contains additional intermediate files. Description of the contents can be found here |
| call_mtSNV_mitoCaller |
*mitoCaller.tsv |
main |
Contains mtDNA variants (i.e., homoplasmies and heteroplasmies) |
| call_mtSNV_mitoCaller |
*mitoCaller.tsv |
intermediate |
gzipped tsv file |
| convert_mitoCaller2VCF |
*.vcf |
main |
2 *.VCF files containing mitoCaller calls in more legible format |
| call_heteroplasmy |
*.tsv |
main |
a *.tsv table showing differences in the normal genotype vs tumor genotype. It also gives heteroplasmy_fraction if there is any. |