Description

Phase vcf panel with Shapeit5 tools

Input

name
description
pattern

meta

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

ch_vcf

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) ]

ch_ref

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

ch_scaffold

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

ch_map

File containing the genetic map.

Output

name
description
pattern

meta

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

bed

BED file containing the windows

*.bed

variants_phased

Phased haplotypes in VCF/BCF format.

*.{vcf,bcf,vcf.gz,bcf.gz}

variants_index

CSI bcftools index

*.csi

versions

File containing software versions

versions.yml