LD analysis in PLINK examines genetic variant associations within populations
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
meta is associated to PLINK native files input
bed{:bash}
:file
PLINK binary biallelic genotype table file
*.{bed}
bim{:bash}
:file
PLINK extended MAP file
*.{bim}
fam{:bash}
:file
PLINK sample information file
*.{fam}
meta2{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
meta2 is associated to VCF files input
vcf{:bash}
:file
VCF format input file
*.{vcf} | *{vcf.gz}
meta3{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
meta is associated to BCF files input
bcf{:bash}
:file
BCF format input file
*.{bcf}
meta4{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
meta is associated to randomly selected snp files input
snpfile{:bash}
:file
randomly selected snp identifiers, used to calculate linkage disequilibrium
*.{txt}
Output
name:type
description
pattern
ld{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*.ld{:bash}
: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{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*.log{:bash}
:file
Log file of the ld process
nosex{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*.nosex{:bash}
:file
Ambiguous sex ID file
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
plink
GPL
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
