Description

Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.

Input

name:type
description
pattern

meta

:map

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

depth

:file

Output from samtools depth (with header)

*

sample_list_file

:file

File containing the list of samples to be processed.

Output

name:type
description
pattern

json

meta

:map

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

*.json

:file

JSON formatted table of relative coverages on the X and Y, with associated error bars.

*.json

tsv

meta

:map

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

*.tsv

:file

TSV table of relative coverages on the X and Y, with associated error bars.

*.tsv

versions_sexdeterrmine

${task.process}

:string

The name of the process

sexdeterrmine

:string

The name of the tool

sexdeterrmine --version 2>&1

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

sexdeterrmine

:string

The name of the tool

sexdeterrmine --version 2>&1

:eval

The expression to obtain the version of the tool

Tools

sexdeterrmine
GPL v3

A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data.

github.com/TCLamnidis/Sex.DetERRmine 10.1038/s41467-018-07483-5
maintainer
Github user TCLamnidis
get in touch
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