subworkflows/vcf_phase_shapeit5

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

Target dataset in VCF/BCF format defined at all variable positions.
Index file of the input VCF/BCF file containing genotype likelihoods.
Pedigree information in the following format: offspring father mother.
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
Structure: [ val(meta), path(vcf), path(csi), path(pedigree), val(region) ]

Reference panel of haplotypes in VCF/BCF format.
Index file of the Reference panel file.
Structure: [ val(meta), path(ref), path(csi) ]

Scaffold of haplotypes in VCF/BCF format.
Index file of the Scaffold of haplotypes file.
Structure: [ val(meta), path(scaffold), path(csi) ]

File containing the genetic map.