Description

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

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.

*.gmap

Output

Name (Type)
Description
Pattern

meta (map)

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

]

phased_variants (file)

Phased haplotypes in VCF/BCF format.

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

versions (file)

File containing software versions

versions.yml
included in
phaseimpute
maintainer
Github user LouisLeNezet
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