modules/beagle5_beagle

Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers.

phasingimputationgenotype

https://github.com/nf-core/modules/[...]/modules/nf-core/beagle5/beagle

Description

Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers.

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

target VCF input file to be imputed and or phased

*.{vcf,vcf.gz}

`vcf_index`
`:file`

target VCF input file index

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

`refpanel`
`:file`

target reference panel

*.{vcf,vcf.gz}

`refpanel_index`
`:file`

target reference panel index

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

`genmap`
`:file`

a PLINK format genetic map with cM units

*.{map,map.gz,map.zip}

`exclsamples`
`:file`

text file containing samples one sample per line to be excluded from the analysis

*.*

`exclmarkers`
`:file`

text file containing markers one marker per line to be excluded from the analysis

*.*

`region`
`:string`

Region to perform imputation

(chr)?\d*:\d*-\d*

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples

*.vcf.gz

`log`

`meta`
`:map`

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

`*.log`
`:file`

a summary of the analysis that includes the Beagle version, the command line arguments, and compute time.

*.log

`versions_beagle`

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

The name of the process

`beagle`
`:string`

The name of the tool

`beagle 2>&1 | sed -n 's/.version $[^)]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`beagle`
`:string`

The name of the tool

`beagle 2>&1 | sed -n 's/.version $[^)]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

beagle5
GPL v3

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

faculty.washington.edu/browning/beagle/beagle faculty.washington.edu/browning/beagle/beagle_5.5_17Dec24.pdf 10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015

modules/beagle5_beagle

Description

Input

`meta`
`:map`

`vcf`
`:file`

`vcf_index`
`:file`

`refpanel`
`:file`

`refpanel_index`
`:file`

`genmap`
`:file`

`exclsamples`
`:file`

`exclmarkers`
`:file`

`region`
`:string`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_beagle`

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

`beagle`
`:string`

`beagle 2>&1 | sed -n 's/.version \([^)]\).*/\1/p'`
`:eval`

Topics

`versions`

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

`beagle`
`:string`

`beagle 2>&1 | sed -n 's/.version \([^)]\).*/\1/p'`
`:eval`

Tools

beagle5
GPL v3

included in

maintainer

get in touch

modules/beagle5_beagle

Description

Input

meta:map

vcf:file

vcf_index:file

refpanel:file

refpanel_index:file

genmap:file

exclsamples:file

exclmarkers:file

region:string

Output

vcf

meta:map

*.vcf.gz:file

log

meta:map

*.log:file

versions_beagle

${task.process}:string

beagle:string

beagle 2>&1 | sed -n 's/.*version \([^)]*\).*/\1/p':eval

Topics

versions

${task.process}:string

beagle:string

beagle 2>&1 | sed -n 's/.*version \([^)]*\).*/\1/p':eval

Tools

beagle5 GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`vcf_index`
`:file`

`refpanel`
`:file`

`refpanel_index`
`:file`

`genmap`
`:file`

`exclsamples`
`:file`

`exclmarkers`
`:file`

`region`
`:string`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_beagle`

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

`beagle`
`:string`

`beagle 2>&1 | sed -n 's/.version \([^)]\).*/\1/p'`
`:eval`

`versions`

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

`beagle`
`:string`

`beagle 2>&1 | sed -n 's/.version \([^)]\).*/\1/p'`
`:eval`

beagle5
GPL v3