nf-core/shapeit5/phaserare @ 0.0.0-0c7146d
Summary
Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2.
Get started
Add the following snippet to your workflow script to include this module.
include { SHAPEIT5_PHASERARE } from 'nf-core/shapeit5/phaserare'
License
MIT License
Name
|
SHAPEIT5_PHASERARE |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
Genotypes to be phased in plain VCF/BCF format. *.{vcf,bcf,vcf.gz,bcf.gz}
|
input_index
file
|
Index file of the input_plain VCF/BCF file containing genotype likelihoods. *.{vcf.gz.csi,bcf.gz.csi}
|
pedigree
file
|
Pedigree information in the following format: offspring father mother. *.{txt, tsv}
|
input_region
string
|
Region to be considered in --input-plain (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. chrXX:leftBufferPosition-rightBufferPosition
|
scaffold
file
|
Scaffold of haplotypes in VCF/BCF format. *.{vcf.gz,bcf.gz}
|
scaffold_index
file
|
Index file of the scaffold file. *.{vcf.gz.csi,bcf.gz.csi}
|
scaffold_region
string
|
Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20). chrXX:leftBufferPosition-rightBufferPosition
|
map
file
|
File containing the genetic map in Glimpse format. *.gmap
|
output_suffix
string
|
Module output format *.{vcf,bcf,vcf.gz,bcf.gz}
|
|---|
phased_variant
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.{vcf,bcf,vcf.gz,bcf.gz}
file
|
Phased variants in VCF/BCF format. *.{vcf,bcf,vcf.gz,bcf.gz}
|
versions_shapeit5
tuple
${task.process}
string
|
The name of the process |
|---|---|
shapeit5
string
|
The name of the tool |
SHAPEIT5_phase_rare | sed "5!d;s/^.*Version *: //; s/ .*$//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| shapeit5 | Fast and accurate method for estimation of haplotypes (phasing) | https://odelaneau.github.io/shapeit5/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:37:34 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fshapeit5%2Fphaserare/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/shapeit5/phaserare/blobs/sha256:887f3e642c3eba16bc447ed52dae40599797d9ab310bd598c6dac8c1aa0b16cd |
| Size | 3.6 KB |
| Checksum | sha256:887f3e642c3eba16bc447ed52dae40599797d9ab310bd598c6dac8c1aa0b16cd |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:45:08 (UTC) | 3 | 3.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:31:00 (UTC) | 3 | 3.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:37:34 (UTC) | 4 | 3.6 KB |