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

*.*

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

versions.yml

:file

File containing software versions

versions.yml

Tools

included in
alleleexpression
maintainer
Github user ashotmarg
get in touch
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