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

]

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

]

*.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

]

*.tsv:file

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

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

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 github.com/TCLamnidis/Sex.DetERRmine/README.md https://github.com/TCLamnidis/Sex.DetERRmine 10.1038/s41467-018-07483-5
Github user TCLamnidis
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