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:false ]

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

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

versions.yml:file

File containing software versions

versions.yml

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
phaseimpute
Github user louislenezet
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