bcftools/bcftools_sort

Sort

VCF

BCF

Description

Sort VCF/BCF file.

Type

bash_script

License

MIT/Expat, GNU

Keywords

Sort

VCF

BCF

Links

Repository

Issues

Documentation

Contributors

Launch

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

Inputs

Name	Type & Properties	Description
--input	file required	Input VCF/BCF file to sort. The file to be sorted by genomic coordinates.

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Write output to a file. If not specified, output goes to standard output.

Name

Type & Properties

--output

-o

file

required

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.

Name

Type & Properties

--output_type

-O

string

--verbosity

-v

integer

--write_index

-W

string