Description

main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

Input VCF/BCF file containing genotype likelihoods.

*.{vcf.gz,bcf.gz}

input_index (file)

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

phased_variants (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}

Tools

glimpse
MIT

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