Description

Defines chunks where to run imputation

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

Target dataset in VCF/BCF format defined at all variable positions.
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).

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

region (string)

Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

txt (file)

Tab delimited output txt file containing buffer and imputation regions.

*.{txt}
author
Github user louislenezet
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Tools

glimpse
MIT

GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.

odelaneau.github.io/GLIMPSE odelaneau.github.io/GLIMPSE/commands https://github.com/odelaneau/GLIMPSE 10.1038/s41588-020-00756-0