bedtools/bedtools_merge

Merge

Overlapping

BED

GFF

VCF

Intervals

Description

Merges overlapping BED/GFF/VCF entries into single intervals.

This tool combines overlapping or book-ended features in BED, GFF, or VCF
files into single merged intervals. It provides extensive options for
controlling merge behavior, including strand-specific merging, distance
thresholds, and aggregation operations on additional columns.

Default behavior: Merges overlapping and adjacent features regardless of strand
Input requirements: Input file must be sorted by chromosome and start position

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file in BED, GFF, or VCF format to be merged. Requirements: - File must be sorted by chromosome and start position - Use `bedtools sort` if input is not sorted Supported formats: BED, GFF, VCF, or BAM (with --bed flag)

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file containing merged intervals. The output will contain merged intervals in BED format, with additional columns included if aggregation operations are specified via --columns and --operation parameters.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--strand -s	boolean_true	Force strandedness for merging operations. Only merge features that are on the same strand. Features on opposite strands will be treated as separate and not merged, even if they overlap. Default: Merging ignores strand information
--specific_strand -S	string	Merge features from one specific strand only. Options: - "+" : Merge only forward strand features - "-" : Merge only reverse strand features Features from the opposite strand will be ignored entirely.
--distance -d	integer	Maximum distance between features for merging. Positive values: Features within this distance will be merged Negative values: Minimum overlap required (in base pairs) Zero (default): Only overlapping and book-ended features merge Examples: - `-d 100` : Merge features within 100bp of each other - `-d -50` : Require at least 50bp overlap to merge
--columns -c	string	Columns to aggregate during merging operations. Specify which columns from the input file should be included in the merged output with aggregation operations applied. Format: Single column (e.g., "5") or comma-separated list (e.g., "4,5,6") Column numbering: 1-indexed (column 1 = chromosome, etc.)
--operation -o	string	Aggregation operations to apply to specified columns. Numerical operations: - sum, min, max, mean, median, mode - absmin, absmax, stdev, sstdev List operations: - collapse (comma-separated list with duplicates) - distinct (comma-separated unique values) - distinct_sort_num (unique values, numerically sorted) Count operations: - count (number of values) - count_distinct (number of unique values) Positional operations: - first (first value), last (last value) Multiple operations: Use comma-separated list (e.g., "sum,mean,count")
--delimiter -delim	string	Custom delimiter for collapse/distinct operations. Character or string used to separate values in list-type operations like collapse, distinct, etc.
--precision -prec	integer	Decimal precision for numerical output values. Controls the number of decimal places displayed for floating-point results from numerical operations.
--bed	boolean_true	Output in BED format when using BAM input. When the input file is in BAM format, this flag ensures the output is written in standard BED format instead of the default BAM-specific output format.
--header	boolean_true	Include header from input file in output. Preserves and prints any header lines from the input file (e.g., GFF version lines, VCF headers) before the merged results.
--no_buffer -nobuf	boolean_true	Disable buffered output for real-time processing. Default behavior: Output is buffered for efficiency With --no_buffer: Each line printed immediately as generated Use cases: Real-time processing, piping to other tools Performance: Slower for large files but enables streaming

Name

Type & Properties

--strand

-s

boolean_true

--specific_strand

-S

string

--distance

-d

integer

--columns

-c

string

--operation

-o

string

--delimiter

-delim

string

--precision

-prec

integer

--bed

boolean_true

--header

boolean_true

--no_buffer

-nobuf

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bed"  
distance: [ 0 ]  
delimiter: [ "," ]  
precision: [ 5 ]  
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_merge/main.nf \  
  -params-file params.yaml

bedtools/bedtools_merge

Inputs

Outputs

Options

Run this component

Relationships

Used by

Uses