bedtools/bedtools_closest

Closest

Nearest

Distance

BED

GFF

VCF

Association

Description

Find the closest feature in file B for each feature in file A.

For each interval in file A, this tool identifies the nearest feature in
file B, regardless of whether they overlap. Useful for associating genomic
features with their nearest neighbors, such as finding the closest gene
to each SNP or the nearest regulatory element to each promoter.

Default behavior: Reports closest feature regardless of strand or overlap
Distance reporting: Optional distance calculation with various orientations
Multiple hits: Configurable handling of ties and k-nearest neighbors

Type

bash_script

License

MIT

Keywords

Closest

Nearest

Distance

BED

GFF

VCF

Association

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"  
k_closest: [ 1 ]  
tie_mode: [ "all" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bedtools/bedtools_closest/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_a -a	file required	Query file in BED, GFF, or VCF format. For each feature in this file, the closest feature in file B will be identified and reported.
--input_b -b	file required multiple	Database file(s) in BED, GFF, or VCF format. Single file: Find closest features in one database Multiple files: Find closest features across multiple databases Format: Same or different format as input A

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with closest feature results. Contains input A features with additional columns showing the closest features from file(s) B, and optionally distance and other metadata.

Name

Type & Properties

--output

file

required

output

Distance Options

Name	Type & Properties	Description
--distance -d	boolean_true	Report distance to closest feature as extra column. Distance calculation: Always positive, 0 for overlapping features Use case: When you need quantitative proximity measurements
--distance_mode -D	string	Report signed distance with orientation awareness. "ref": Distance relative to reference genome coordinates "a": Distance relative to strand of feature A "b": Distance relative to strand of feature B Negative values: Upstream features Positive values: Downstream features

Name

Type & Properties

--distance

-d

boolean_true

--distance_mode

-D

string

Filtering Options

Name	Type & Properties	Description
--ignore_overlaps -io	boolean_true	Ignore overlapping features in B. Only consider features in B that do not overlap with A. Useful for finding nearby but non-overlapping features.
--ignore_upstream -iu	boolean_true	Ignore upstream features in B. Requires: --distance_mode parameter Effect: Only consider downstream features Orientation: Follows --distance_mode orientation rules
--ignore_downstream -id	boolean_true	Ignore downstream features in B. Requires: --distance_mode parameter Effect: Only consider upstream features Orientation: Follows --distance_mode orientation rules
--force_upstream -fu	boolean_true	Choose first upstream feature when ties exist. Requires: --distance_mode parameter Tie handling: Among equally close features, prefer upstream Orientation: Follows --distance_mode orientation rules
--force_downstream -fd	boolean_true	Choose first downstream feature when ties exist. Requires: --distance_mode parameter Tie handling: Among equally close features, prefer downstream Orientation: Follows --distance_mode orientation rules
--strand -s	boolean_true	Require same strandedness. Only consider features in B that are on the same strand as the corresponding feature in A.
--different_strand -S	boolean_true	Require different strandedness. Only consider features in B that are on the opposite strand from the corresponding feature in A.

Name

Type & Properties

--ignore_overlaps

-io

boolean_true

--ignore_upstream

-iu

boolean_true

--ignore_downstream

-id

boolean_true

--force_upstream

-fu

boolean_true

--force_downstream

-fd

boolean_true

--strand

-s

boolean_true

--different_strand

-S

boolean_true

Advanced Options

Name	Type & Properties	Description
--k_closest -k	integer	Report k closest hits for each query. Default: 1 (single closest feature) Multiple hits: Reports multiple closest features per query Tie handling: All ties still reported based on --tie_mode
--tie_mode -t	string	How to handle ties for closest features. "all": Report all equally close features (default) "first": Report first tie found in file B "last": Report last tie found in file B
--different_names -N	boolean_true	Require different names between query and hit. For BED files, compares the 4th column (name field). Useful to avoid self-hits in self-comparisons.

Name

Type & Properties

--k_closest

-k

integer

--tie_mode

-t

string

--different_names

-N

boolean_true