Generate Hardy-Weinberg statistics for provided input
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}
PLINK extended MAP file
*.{bim}
fam{:bash}
PLINK sample information file
*.{fam}
meta2{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ] meta2 is associated to VCF files input
vcf{:bash}
VCF format input file
*.{vcf} | *{vcf.gz}
meta3{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ] meta is associated to BCF files input
bcf{:bash}
BCF format input file
*.{bcf}
hwe{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.hwe{:bash}
Summary file containing observed vs expected heterozygous frequencies and the p-value of the hardy-weinberg statistics
versions_plink{:bash}
${task.process}{:bash}
:string
The name of the process
plink{:bash}
The name of the tool
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
