modules/shapeit5_ligate

Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.

ligatehaplotypeshapeit

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

Description

Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.

Input

name:type

description

pattern

`meta`
`:map`

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

`input_list`
`:file`

VCF/BCF files containing genotype probabilities (GP field). The files should be ordered by genomic position.

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

`input_list_index`
`:file`

VCF/BCF files index.

*.csi

`suffix_`
`:string`

Output format

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

Output

name:type

description

pattern

`merged_variants`

`meta`
`:map`

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

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

Output VCF/BCF file for the merged regions. Phased information (HS field) is updated accordingly for the full region.

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

`versions_shapeit5`

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

The name of the process

`shapeit5`
`:string`

The name of the tool

`SHAPEIT5_ligate | 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_ligate | 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)

odelaneau.github.io/shapeit5 odelaneau.github.io/shapeit5/docs/documentation https://github.com/odelaneau/shapeit5 10.1101/2022.10.19.512867

modules/shapeit5_ligate

Description

Input

`meta`
`:map`

`input_list`
`:file`

`input_list_index`
`:file`

`suffix_`
`:string`

Output

`merged_variants`

`meta`
`:map`

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

`versions_shapeit5`

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

`shapeit5`
`:string`

`SHAPEIT5_ligate | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

Topics

`versions`

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

`shapeit5`
`:string`

`SHAPEIT5_ligate | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

Tools

shapeit5
MIT

included in

maintainer

get in touch

modules/shapeit5_ligate

Description

Input

meta:map

input_list:file

input_list_index:file

suffix_:string

Output

merged_variants

meta:map

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

versions_shapeit5

${task.process}:string

shapeit5:string

SHAPEIT5_ligate | sed "5!d;s/^.*Version *: //; s/ .*$//":eval

Topics

versions

${task.process}:string

shapeit5:string

SHAPEIT5_ligate | sed "5!d;s/^.*Version *: //; s/ .*$//":eval

Tools

shapeit5 MIT

included in

maintainer

get in touch

`meta`
`:map`

`input_list`
`:file`

`input_list_index`
`:file`

`suffix_`
`:string`

`merged_variants`

`meta`
`:map`

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

`versions_shapeit5`

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

`shapeit5`
`:string`

`SHAPEIT5_ligate | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

`versions`

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

`shapeit5`
`:string`

`SHAPEIT5_ligate | sed "5!d;s/^.Version : //; s/ .*$//"`
`:eval`

shapeit5
MIT