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
]
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
meta2:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
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}
meta3:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
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}
meta4:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
map:file
File containing the genetic map.
*.gmap
Output
name:type
description
pattern
phased_variant
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.{vcf,bcf,vcf.gz,bcf.gz}:file
Phased variant dataset in VCF/BCF format.
*.{vcf,bcf,vcf.gz,bcf.gz}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
shapeit5
MIT
Fast and accurate method for estimation of haplotypes (phasing)
