Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input
:file
Target dataset in VCF/BCF format defined at all variable positions.
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
*.{vcf,bcf,vcf.gz,bcf.gz}
input_index
:file
Index file of the input VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
pedigree
:file
Pedigree information in the following format: offspring father mother.
*.{txt, tsv}
region
:string
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
chrXX:leftBufferPosition-rightBufferPosition
reference
:file
Reference panel of haplotypes in VCF/BCF format.
*.{vcf.gz,bcf.gz}
reference_index
:file
Index file of the Reference panel file.
*.{vcf.gz.csi,bcf.gz.csi}
scaffold
:file
Scaffold of haplotypes in VCF/BCF format.
*.{vcf.gz,bcf.gz}
scaffold_index
:file
Index file of the scaffold file.
*.{vcf.gz.csi,bcf.gz.csi}
map
:file
File containing the genetic map in Glimpse format.
*.gmap
Output
name:type
description
pattern
phased_variant
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{bcf,graph,bh}
:file
Phased variant dataset in BCF, GRAPH or XCF binary format.
*.{bcf,graph,bh}
versions_shapeit5
${task.process}
:string
The name of the process
shapeit5
:string
The name of the tool
SHAPEIT5_phase_common | sed "5!d;s/^.*Version *: //; s/ .*$//"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
shapeit5
:string
The name of the tool
SHAPEIT5_phase_common | sed "5!d;s/^.*Version *: //; s/ .*$//"
:eval
The expression to obtain the version of the tool
Tools
shapeit5
MIT
Fast and accurate method for estimation of haplotypes (phasing)
