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:false ]

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

mtnucratio

meta

:map

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

*.mtnucratio

:file

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

*.mtnucratio

json

meta

:map

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

*.json

:file

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

*.json

versions_mtnucratio

${task.process}

:string

The name of the process

mtnucratio

:string

The name of the tool

mtnucratio --version 2>&1 | sed -n 's/Version: //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

mtnucratio

:string

The name of the tool

mtnucratio --version 2>&1 | sed -n 's/Version: //p'

:eval

The expression to obtain the version of the tool

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
maintainer
Github user louperelo
get in touch
Ask a question on Slack Open an issue on GitHub