Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input{:bash}
: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}
input_index{:bash}
:file
Index file for the input VCF/BCF file.
region{:bash}
: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
chunk_chr{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.txt{:bash}
:file
Tab delimited output txt file containing buffer and imputation regions.
*.txt
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
glimpse
MIT
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
