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)

*

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

json (file)

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

*.json

tsv (file)

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

*.tsv
maintainer
Github user TCLamnidis
get in touch
Ask a question on Slack Open an issue on GitHub

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