nf-core/bcftools/pluginsetgt @ 0.0.0-0c7146d
Summary
Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
Get started
Add the following snippet to your workflow script to include this module.
include { BCFTOOLS_PLUGINSETGT } from 'nf-core/bcftools/pluginsetgt'
License
MIT License
Name
|
BCFTOOLS_PLUGINSETGT |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
vcf
file
|
The vcf file to be inspected. e.g. 'file.vcf' |
index
file
|
The tab index for the VCF file to be inspected. e.g. 'file.tbi' |
target_gt
string
|
Genotypes to change |
|---|
new_gt
string
|
Genotypes to set |
|---|
regions
file
|
Optionally, restrict the operation to regions listed in this file. e.g. 'file.vcf' |
|---|
targets
file
|
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) e.g. 'file.vcf' |
|---|
csi
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.csi
file
|
Default VCF file index *.csi
|
tbi
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tbi
file
|
Alternative VCF file index *.tbi
|
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.{vcf,vcf.gz,bcf,bcf.gz}
file
|
VCF output file containing set genotypes *.{vcf,vcf.gz,bcf,bcf.gz}
|
versions_bcftools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
bcftools
string
|
The tool name |
bcftools --version | sed '1!d; s/^.*bcftools //'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bcftools | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. | https://samtools.github.io/bcftools/howtos/index.html |
| bcftools plugin setGT | Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that. | https://samtools.github.io/bcftools/howtos/plugins.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:25:30 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fpluginsetgt/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bcftools/pluginsetgt/blobs/sha256:2a417c21ec8caad4b23e72af60152ce997c4321d31b541a33697dfe8a30a19e4 |
| Size | 4.3 KB |
| Checksum | sha256:2a417c21ec8caad4b23e72af60152ce997c4321d31b541a33697dfe8a30a19e4 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d |