modules/shapeit5_phaserare

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

phasingrare variantshaplotypeshapeit

https://github.com/nf-core/modules/[...]/modules/nf-core/shapeit5/phaserare

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

`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 in Glimpse format.

*.gmap

`output_suffix`
`:string`

Module output format

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

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_shapeit5`

`${task.process}`
`:string`

The name of the process

`shapeit5`
`:string`

The name of the tool

`SHAPEIT5_phase_rare | 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_rare | 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)

github.com/odelaneau/shapeit5 10.1101/2022.10.19.512867

modules/shapeit5_phaserare

Description

Input

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`pedigree`
`:file`

`input_region`
`:string`

`scaffold`
`:file`

`scaffold_index`
`:file`

`scaffold_region`
`:string`

`map`
`:file`

`output_suffix`
`:string`

Output

`phased_variant`

`meta`
`:map`

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

`versions_shapeit5`

`${task.process}`
`:string`

`shapeit5`
`:string`

`SHAPEIT5_phase_rare | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`shapeit5`
`:string`

`SHAPEIT5_phase_rare | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

Tools

shapeit5
MIT

maintainer

get in touch

modules/shapeit5_phaserare

Description

Input

meta :map

input :file

input_index :file

pedigree :file

input_region :string

scaffold :file

scaffold_index :file

scaffold_region :string

map :file

output_suffix :string

Output

phased_variant

meta :map

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

versions_shapeit5

${task.process} :string

shapeit5 :string

SHAPEIT5_phase_rare | sed "5!d;s/^.*Version *: //; s/ .*$//" :eval

Topics

versions

${task.process} :string

shapeit5 :string

SHAPEIT5_phase_rare | sed "5!d;s/^.*Version *: //; s/ .*$//" :eval

Tools

shapeit5MIT

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`pedigree`
`:file`

`input_region`
`:string`

`scaffold`
`:file`

`scaffold_index`
`:file`

`scaffold_region`
`:string`

`map`
`:file`

`output_suffix`
`:string`

`phased_variant`

`meta`
`:map`

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

`versions_shapeit5`

`${task.process}`
`:string`

`shapeit5`
`:string`

`SHAPEIT5_phase_rare | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

`versions`

`${task.process}`
`:string`

`shapeit5`
`:string`

`SHAPEIT5_phase_rare | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

shapeit5
MIT