bedtools/bedtools_map

genomics

intervals

map

statistics

aggregate

annotate

overlap

scores

Description

Apply statistical functions to columns from overlapping genomic intervals.

This tool maps values from intervals in file B onto overlapping intervals in file A
by applying statistical operations (sum, mean, median, etc.). For each interval in A,
it finds all overlapping intervals in B and applies the specified function to the
specified column(s). Useful for aggregating scores, computing statistics over
genomic regions, or annotating intervals with quantitative data.

Type

bash_script

License

MIT

Keywords

genomics

intervals

map

statistics

aggregate

annotate

overlap

scores

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 v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_map/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_a -a	file required	First input file (intervals to annotate). Format: BED, GFF, VCF file with genomic intervals Requirement: Must be sorted by chromosome, then start position Usage: Each interval will be annotated with mapped values from file B
--input_b -b	file required	Second input file (source of values to map). Format: BED, GFF, VCF file with genomic intervals and data columns Requirement: Must be sorted by chromosome, then start position Usage: Overlapping intervals provide values for mapping operations

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with mapped values appended to input A intervals. Format: Same as input A with additional columns for mapped values Content: Original columns from A plus computed statistical values Order: Follows the order specified in column and operation parameters

Name

Type & Properties

--output

file

required

output

Mapping Options

Name	Type & Properties	Description
--columns -c	string	Columns from file B to use for mapping operations. Default: 5 (fifth column, typically score column in BED) Format: Comma-delimited list for multiple columns Example: "5" for score column, "4,5" for name and score columns Indexing: 1-based column numbering
--operations -o	string	Statistical operations to apply to specified columns. Numeric operations: sum, min, max, absmin, absmax, mean, median, mode, antimode, stdev, sstdev, count, count_distinct List operations: collapse, distinct, distinct_sort_num, distinct_sort_num_desc, distinct_only Position operations: first, last Default: sum Format: Comma-delimited list for multiple operations Pairing: Operations applied to columns in respective order
--delimiter -delim	string	Custom delimiter for collapse operations. Default: "," (comma) Usage: Only affects collapse, distinct, and related operations Example: "\|" for pipe-separated values, ";" for semicolon-separated
--precision -prec	integer	Decimal precision for numerical output. Default: 5 decimal places Range: 0-15 (reasonable range for floating point precision) Usage: Controls rounding of computed statistical values

Name

Type & Properties

--columns

-c

string

--operations

-o

string

--delimiter

-delim

string

--precision

-prec

integer

Overlap Options

Name	Type & Properties	Description
--min_overlap_a -f	double	Minimum overlap required as fraction of A. Range: 0.0 to 1.0 Default: 1E-9 (effectively 1bp) Example: 0.50 requires 50% of A to be overlapped by B
--min_overlap_b -F	double	Minimum overlap required as fraction of B. Range: 0.0 to 1.0 Default: 1E-9 (effectively 1bp) Example: 0.50 requires 50% of B to overlap A
--reciprocal -r	boolean_true	Require reciprocal overlap for both A and B. Effect: Both -f and -F thresholds must be satisfied Example: With -f 0.90 -r, requires B overlaps 90% of A AND A overlaps 90% of B Default: false
--either -e	boolean_true	Require minimum fraction satisfied for A OR B. Effect: Only one of -f or -F thresholds needs to be satisfied Alternative: Without -e, both fractions must be satisfied Default: false (both required)

Name

Type & Properties

--min_overlap_a

-f

double

--min_overlap_b

-F

double

--reciprocal

-r

boolean_true

--either

-e

boolean_true

Strand Options

Name	Type & Properties	Description
--same_strand -s	boolean_true	Require same strandedness for overlaps. Effect: Only consider overlaps on the same strand Default: false (strand-independent)
--opposite_strand -S	boolean_true	Require different strandedness for overlaps. Effect: Only consider overlaps on opposite strands Default: false (strand-independent) Note: May have issues in some bedtools versions

Name

Type & Properties

--same_strand

-s

boolean_true

--opposite_strand

-S

boolean_true

Format Options

Name	Type & Properties	Description
--split	boolean_true	Treat split BAM or BED12 entries as distinct intervals. Effect: Split multi-block entries into individual intervals Usage: For BAM alignments with gaps or BED12 entries Default: false
--bed_output --bed	boolean_true	Write output in BED format when using BAM input. Effect: Forces BED output format for BAM inputs Default: false
--header	boolean_true	Print header from file A prior to results. Effect: Includes original header from input file A Default: false

Name

Type & Properties

--split

boolean_true

--bed_output

--bed

boolean_true

--header

boolean_true

Advanced Options

Name	Type & Properties	Description
--genome -g	file	Genome file for consistent chromosome sorting. Format: Tab-delimited file with chromosome name and size Usage: Only applies when used with sorted data Purpose: Enforces consistent chromosome sort order
--no_name_check --nonamecheck	boolean_true	Skip chromosome naming convention checks for sorted data. Effect: Allows different naming (e.g., "chr1" vs "chr01") Usage: For files with inconsistent chromosome naming Default: false (strict checking)
--no_buffer --nobuf	boolean_true	Disable buffered output. Effect: Print each line immediately instead of buffering Usage: For real-time processing or piping Trade-off: Slower performance but immediate output Default: false (buffered output)
--io_buffer --iobuf	string	Specify input buffer memory size. Format: Integer with optional K/M/G suffix Example: "128M" for 128 megabytes Note: No effect with compressed files

Name

Type & Properties

--genome

-g

file

--no_name_check

--nonamecheck

boolean_true

--no_buffer

--nobuf

boolean_true

--io_buffer

--iobuf

string