bcftools/bcftools_sort
Sort
VCF
BCF
Description
Sort VCF/BCF file.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input VCF/BCF file to sort. The file to be sorted by genomic coordinates. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Write output to a file. If not specified, output goes to standard output. |
Options
Name | Type & Properties | Description |
|---|---|---|
--output_type -O | string | Output file type. **Options:** - u: uncompressed BCF - b: compressed BCF - v: uncompressed VCF - z: compressed VCF - 0-9: compression level for compressed formats **Default:** v (uncompressed VCF) |
--verbosity -v | integer | Verbosity level. Higher values increase verbosity of output messages. |
--write_index -W | string | Automatically index the output files. **Format:** Specify index format or use default. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.gz"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.1 \
-main-script target/nextflow/bcftools/bcftools_sort/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bcftools/bcftools_sortbiobox v0.4.1
Uses
0 relationships
No component dependencies found.