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}
input_index:file
Index file of the input VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
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.
map:file
File containing the genetic map.
*.gmap
model:string
Algorithm model to use:
“recursive”: Recursive algorithm
“sequential”: Sequential algorithm (Recommended)
“uniform-number-variants”: Experimental. Uniform the number of variants in the sequential algorithm
{recursive,sequential,uniform-number-variants}
Output
name:type
description
pattern
chunk_chr
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.txt:file
Tab delimited output txt file containing buffer and imputation regions.
*.{txt}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
glimpse2
MIT
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
