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:false ]

input:file

Genotypes to be phased in plain VCF/BCF format.

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

input_index:file

Index file of the input_plain 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}

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

meta2:map

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

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

meta3:map

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

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:false ]

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

Phased variants in VCF/BCF format.

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

versions

versions.yml:file

File containing software versions

versions.yml

Tools

Github user LouisLeNezet
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