Description

Provide the SNP coverage of each individual in an eigenstrat formatted dataset.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

geno (file)

An Eigenstrat formatted genotype file

*.{geno}

snp (file)

An Eigenstrat formatted snp file

*.{snp}

ind (file)

An Eigenstrat formatted individual file

*.{ind}

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

tsv (file)

A TSV table with the number of covered SNPs per individual.

*.{tsv}

json (file)

A json table with the number of covered SNPs per individual.

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

Tools

eigenstratdatabasetools
GPL v3

A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.

github.com/TCLamnidis/EigenStratDatabaseTools/README.md https://github.com/TCLamnidis/EigenStratDatabaseTools