Description

A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

(coordinate) sorted BAM/SAM file

*.{bam,sam}

mt_id (string)

Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

mtnucratio (file)

Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)

*.mtnucratio

json (file)

JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file

*.json
author
Github user louperelo
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Tools

mtnucratio
GPL v3

A small tool to determine MT to Nuclear ratios for NGS data.

github.com/apeltzer/MTNucRatioCalculator 10.1186/s13059-016-0918-z