Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

geno{:bash}

:file

An Eigenstrat formatted genotype file

*.{geno}

snp{:bash}

:file

An Eigenstrat formatted snp file

*.{snp}

ind{:bash}

:file

An Eigenstrat formatted individual file

*.{ind}

Output

name:type
description
pattern

tsv{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

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

*.{tsv}

json{:bash}

meta{:bash}

:map

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

*.json{:bash}

:file

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

*.{json}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainer
Github user TCLamnidis
get in touch
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