Description

Beagle v5.2 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}

ref (file)

reference panel in bref3 or VCF format

*.{vcf,vcf.gz,bref3}

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

meta (map)

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

versions (file)

File containing software versions

versions.yml

vcf (file)

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

*.vcf.gz

log (file)

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

*.log
author
Github user ashotmarg
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

beagle5
GPL v3

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

faculty.washington.edu/browning/beagle/b5_2 faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf 10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015