Description

Subset plink pfiles 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:false ]

pgen:file

PLINK 2 binary genotype table

*.{pgen}

psam:file

PLINK 2 sample information file

*.{psam}

pvar:file

PLINK 2 variant information file

*.{pvar}

variants:file

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

*.{keep}

Output

name:type
description
pattern

extract_pgen

meta:map

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

*.pgen:file

PLINK 2 binary genotype table, containing extracted variants

*.{pgen}

extract_psam

meta:map

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

*.psam:file

PLINK 2 sample information file associated with the extracted data

*.{psam}

extract_pvar

meta:map

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

*.pvar.zst:file

PLINK 2 variant information file, containing extracted variants

*.{pvar.zst}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

plink2
GPL v3

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