Description

Subset plink bfiles with a text file of variant identifiers

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

PLINK binary biallelic genotype table

*.{bed}

bim (file)

PLINK extended MAP file

*.{bim}

fam (file)

PLINK sample information file

*.{fam}

variants (file)

A text file containing variant identifiers to keep (one per line)

*.{keep}

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

bed (file)

PLINK binary biallelic genotype table

*.{bed}

bim (file)

PLINK extended MAP file

*.{bim}

fam (file)

PLINK sample information file

*.{fam}
author
Github user nebfield
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

plink
GPL

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

cog-genomics.org/plink