nf-core/glimpse2/phase @ 0.0.0-6c4ed3a
Summary
Tool for imputation and phasing from vcf file or directly from bam files.
Get started
Add the following snippet to your workflow script to include this module.
include { GLIMPSE2_PHASE } from 'nf-core/glimpse2/phase'
License
MIT License
Name
|
GLIMPSE2_PHASE |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
input
file
|
Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods. When using BAM/CRAM the name of the file is used as samples name. *.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}
|
input_index
file
|
Index file of the input BAM/CRAM/VCF/BCF file. *.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}
|
bamlist
file
|
File containing the list of BAM/CRAM files to be phased. One file per line and a second column can be added to indicate the sample name. *.{txt,tsv}
|
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). Optional if reference panel is in bin format. chrXX:leftBufferPosition-rightBufferPosition
|
output_region
string
|
Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). Optional if reference panel is in bin format. 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. Optional if reference panel is in bin format. *.gmap
|
meta2
map
|
Groovy Map containing genomic map information e.g. |
|---|---|
fasta_reference
file
|
Faidx-indexed reference sequence file in the appropriate genome build. Necessary for CRAM files. *.fasta
|
fasta_reference_index
file
|
Faidx index of the reference sequence file in the appropriate genome build. Necessary for CRAM files. *.fai
|
stats_coverage
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.txt.gz
file
|
Optional coverage statistic file created when BAM/CRAM files are used as inputs. *.txt.gz
|
phased_variants
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.{vcf,vcf.gz,bcf,bgen}
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_glimpse2
tuple
${task.process}
string
|
The name of the process |
|---|---|
glimpse2
string
|
The name of the tool |
GLIMPSE2_phase --help | grep -oE 'v[0-9.]+' | cut -c2-
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| glimpse2 | GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies. | https://odelaneau.github.io/GLIMPSE |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:21:40 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fglimpse2%2Fphase/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/glimpse2/phase/blobs/sha256:ab1dbdae8aa319736ad88d48ba4218f0616bc73f3beda4c3fe70 |