bedtools/bedtools_sort

Sort

Sorting

BED

GFF

VCF

Chromosome

Description

Sorts genomic feature files by chromosome and other criteria.

This tool provides flexible sorting options for BED, GFF, and VCF files,
including chromosome-based sorting, feature size sorting, score-based sorting,
and custom chromosome ordering using genome files.

Default behavior: Sorts by chromosome name, then by start position
Custom ordering: Use --genome or --faidx to specify chromosome order

Type

bash_script

License

MIT

Keywords

Sort

Sorting

BED

GFF

VCF

Chromosome

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bed"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bedtools/bedtools_sort/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input genomic feature file to be sorted. Supported formats: BED, GFF, VCF Requirements: File should contain valid genomic intervals Note: File does not need to be pre-sorted

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output file containing sorted genomic features. The output will be in the same format as the input file, with features sorted according to the specified criteria.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--sizeA	boolean_true	Sort by feature size in ascending order. Features are sorted by their span (end - start) from smallest to largest, regardless of chromosome location.
--sizeD	boolean_true	Sort by feature size in descending order. Features are sorted by their span (end - start) from largest to smallest, regardless of chromosome location.
--chrThenSizeA	boolean_true	Sort by chromosome, then by feature size (ascending). Primary sort: Chromosome name (lexicographic) Secondary sort: Feature size (smallest to largest)
--chrThenSizeD	boolean_true	Sort by chromosome, then by feature size (descending). Primary sort: Chromosome name (lexicographic) Secondary sort: Feature size (largest to smallest)
--chrThenScoreA	boolean_true	Sort by chromosome, then by score (ascending). Primary sort: Chromosome name (lexicographic) Secondary sort: Score field (lowest to highest) Requirements: Input must have score column (typically column 5 in BED)
--chrThenScoreD	boolean_true	Sort by chromosome, then by score (descending). Primary sort: Chromosome name (lexicographic) Secondary sort: Score field (highest to lowest) Requirements: Input must have score column (typically column 5 in BED)
--genome -g	file	Custom chromosome ordering file. Text file with one chromosome name per line, defining the desired chromosome order. Features will be sorted according to this order rather than lexicographic sorting. Format: One chromosome name per line (e.g., "chr1", "chr2", etc.)
--faidx	file	FASTA index file for chromosome ordering. Uses a FASTA index file (.fai) to determine chromosome order. The chromosomes will be sorted according to their order in the index file. Format: Standard samtools faidx output format
--header	boolean_true	Preserve header lines in output. Header lines (starting with '#' or other format-specific prefixes) from the input file will be printed before the sorted features.

Name

Type & Properties

--sizeA

boolean_true

--sizeD

boolean_true

--chrThenSizeA

boolean_true

--chrThenSizeD

boolean_true

--chrThenScoreA

boolean_true

--chrThenScoreD

boolean_true

--genome

-g

file

--faidx

file

--header

boolean_true