Description

Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input_plain (file)

Genotypes to be phased in plain VCF/BCF format.

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

input_plain_index (file)

Index file of the input_plain VCF/BCF file containing genotype likelihoods.

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

input_region (string)

Region to be considered in —input-plain (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

pedigree (file)

Pedigree information in the following format: offspring father mother.

*.{txt, tsv}

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}

scaffold_region (string)

Region to be considered in —scaffold (e.g. chr20:1000000-2000000 or chr20).

chrXX:leftBufferPosition-rightBufferPosition

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
maintainer
Github user LouisLeNezet
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