Index file of the input VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
samples_file
:file
File with sample names and ploidy information.
One sample per line with a mandatory second column indicating ploidy (1 or 2).
Sample names that are not present are assumed to have ploidy 2 (diploids).
GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
*.{txt,tsv}
input_region
:string
Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
chrXX:leftBufferPosition-rightBufferPosition
output_region
:string
Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
chrXX:leftBufferPosition-rightBufferPosition
reference
:file
Reference panel of haplotypes in VCF/BCF format.
*.{vcf.gz,bcf.gz}
reference_index
:file
Index file of the Reference panel file.
*.{vcf.gz.csi,bcf.gz.csi}
map
:file
File containing the genetic map.
*.gmap
Output
name:type
description
pattern
phased_variants
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{vcf,bcf,vcf.gz,bcf.gz}
:file
Output VCF/BCF file containing genotype probabilities (GP field),
imputed dosages (DS field), best guess genotypes (GT field),
sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.
*.{vcf,bcf,vcf.gz,bcf.gz}
versions_glimpse
${task.process}
:string
The name of the process
glimpse
:string
The name of the tool
GLIMPSE_phase --help | sed -n '/Version/s/.*: //p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
glimpse
:string
The name of the tool
GLIMPSE_phase --help | sed -n '/Version/s/.*: //p'
:eval
The expression to obtain the version of the tool
Tools
glimpse
MIT
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
