Description

LD analysis in PLINK examines genetic variant associations within populations

Input

Name (Type)
Description
Pattern

meta (map)

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

]
meta is associated to PLINK native files input

meta2 (map)

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

]
meta2 is associated to VCF files input

meta3 (map)

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

]
meta is associated to BCF files input

meta4 (map)

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

]
meta is associated to randomly selected snp files input

bed (file)

PLINK binary biallelic genotype table file

*.{bed}

bim (file)

PLINK extended MAP file

*.{bim}

fam (file)

PLINK sample information file

*.{fam}

vcf (file)

VCF format input file

*.{vcf} | *{vcf.gz}

bcf (file)

BCF format input file

*.{bcf}

snpfile (file)

randomly selected snp identifiers, used to calculate linkage disequilibrium

*.{txt}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

ld (file)

The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².

log (file)

Log file of the ld process

nosex (file)

Ambiguous sex ID file

maintainer
Github user davidebag
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 cog-genomics.org/plink/1.9/data#recode https://www.cog-genomics.org/plink/1.9/dev