Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
meta is associated to the PLINK native file input
bed:file
PLINK binary biallelic genotype table file
*.{bed}
bim:file
PLINK extended MAP file
*.{bim}
fam:file
PLINK sample information file
*.{fam}
meta2:map
Groovy Map containing sample information,
e.g. [ id:‘test’, single_end
]
meta2 is associated to VCF file input
vcf:file
Variant calling file (vcf)
*.{vcf}
meta3:map
Groovy Map containing sample information,
e.g. [ id:‘test’, single_end
]
meta3 is associated to BCF file input
bcf:file
PLINK variant information + sample ID + genotype call binary file
*.{bcf}
meta4:map
Groovy Map containing sample information,
e.g. [ id:‘test’, single_end
]
meta4 is associated to phenotype file input
phe:file
PLINK file containing phenotype information. This phenotype information can be read from the third column with the —pheno option or from a specific column with the —pheno-name option
*.{phe}
Output
name:type
description
pattern
assoc
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.assoc:file
PLINK GWAS association file
*.{assoc}
log
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.log:file
PLINK GWAS association log file
*.{log}
nosex
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.nosex:file
PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option —allow-no-sex
*.{nosex}
versions
versions.yml: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.
