Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

target VCF input file to be imputed and or phased

*.{vcf,vcf.gz}

vcf_index{:bash}

:file

target VCF input file index

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

refpanel{:bash}

:file

target reference panel

*.{vcf,vcf.gz}

refpanel_index{:bash}

:file

target reference panel index

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

genmap{:bash}

:file

a PLINK format genetic map with cM units

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

exclsamples{:bash}

:file

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

*.*

exclmarkers{:bash}

:file

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

*.*

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

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

*.vcf.gz

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

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

*.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
alleleexpressionphaseimpute
maintainer
Github user ashotmarg
get in touch
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