bedtools/bedtools_subtract
genomics
intervals
subtract
remove
overlap
filter
exclusion
Description
Remove the portion(s) of genomic intervals that are overlapped by other features.
bedtools subtract removes portions of intervals in file A that overlap with intervals
in file B. By default, only the overlapping portions are removed, leaving the
non-overlapping parts of A intervals. This is essential for genomic analysis tasks
like removing repetitive elements, excluding known variants, or filtering out
unwanted regions from interval datasets.
This tool is commonly used for:
Removing repetitive elements or low-complexity regions from analysis
Excluding known polymorphic sites from variant calling regions
Filtering out blacklisted genomic regions from ChIP-seq peaks
Creating clean interval sets by removing overlapping annotations
Generating non-overlapping genomic windows for analysis
Quality control by removing problematic genomic regions
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input_a -a | file required | Input file A containing genomic intervals to subtract from. **Format:** BED, GFF, or VCF file with genomic coordinates **Content:** Intervals from which overlapping portions will be removed **Usage:** This is the primary input file that will be modified **Requirements:** Standard genomic interval format **Output:** Modified intervals with overlapping regions removed |
--input_b -b | file required | Input file B containing genomic intervals to subtract. **Format:** BED, GFF, or VCF file with genomic coordinates **Content:** Intervals that will be removed from file A **Usage:** Regions in this file will be subtracted from input_a intervals **Requirements:** Standard genomic interval format **Effect:** Any overlap with these intervals will be removed from A |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file with subtracted intervals. **Format:** Same format as input file A **Content:** Modified intervals from A with B regions removed **Behavior:** Only non-overlapping portions of A intervals are retained **Special cases:** Intervals completely overlapped by B are omitted entirely |
Overlap Options
Name | Type & Properties | Description |
|---|---|---|
--min_overlap_a -f | double | Minimum overlap required as a fraction of A interval. **Default:** 1E-9 (essentially 1 base pair) **Range:** 0.0 to 1.0 **Usage:** B must overlap at least this fraction of A for subtraction **Example:** 0.5 requires B to overlap at least 50% of A interval |
--min_overlap_b -F | double | Minimum overlap required as a fraction of B interval. **Default:** 1E-9 (essentially 1 base pair) **Range:** 0.0 to 1.0 **Usage:** A must overlap at least this fraction of B for subtraction **Example:** 0.3 requires A to overlap at least 30% of B interval |
--reciprocal -r | boolean_true | Require that the fraction overlap be reciprocal for A AND B. **Usage:** Both A and B must overlap each other by the specified fractions **Example:** With -f 0.9, B must overlap 90% of A AND A must overlap 90% of B **Effect:** More stringent overlap requirement than -f or -F alone **Default:** false (only one-way overlap required) |
--either_overlap -e | boolean_true | Require that the minimum fraction be satisfied for A OR B. **Usage:** Either the -f fraction OR the -F fraction must be satisfied **Example:** With -f 0.9 and -F 0.1, either 90% of A OR 10% of B must be covered **Default:** false (both fractions must be satisfied if both specified) |
Strand Options
Name | Type & Properties | Description |
|---|---|---|
--same_strand -s | boolean_true | Require same strandedness for overlap detection. **Usage:** Only subtract B intervals that overlap A on the same strand **Applications:** Strand-specific analysis, gene annotation filtering **Default:** false (overlaps reported without respect to strand) |
--opposite_strand -S | boolean_true | Require different strandedness for overlap detection. **Usage:** Only subtract B intervals that overlap A on the opposite strand **Applications:** Antisense filtering, strand-specific exclusions **Default:** false (overlaps reported without respect to strand) |
Subtraction Behavior
Name | Type & Properties | Description |
|---|---|---|
--remove_entire -A | boolean_true | Remove entire feature if any overlap is found. **Behavior:** Instead of partial subtraction, remove entire A interval if any overlap with B **Usage:** Binary filtering - intervals are either kept completely or removed completely **Applications:** Quality filtering, blacklist exclusion **Default:** false (only overlapping portions are subtracted) |
--remove_if_all_overlap -N | boolean_true | Remove entire feature based on sum of all B feature overlaps. **Usage:** Same as -A but considers cumulative overlap from multiple B features **Behavior:** Remove A if total overlap from all B features meets threshold **Applications:** Complex filtering based on multiple overlapping annotations **Requires:** Used with -f option for fraction threshold |
Output Format Options
Name | Type & Properties | Description |
|---|---|---|
--write_original_b -wb | boolean_true | Write the original entry in B for each overlap. **Output:** Each A interval followed by overlapping B intervals **Usage:** Track which B features caused the subtraction **Restrictions:** Overlap filtering by -f and -r still applies **Applications:** Detailed overlap reporting, annotation tracking |
--write_overlap_counts -wo | boolean_true | Write original A and B entries plus the number of base pairs of overlap. **Output:** A interval, B interval, and overlap count in base pairs **Usage:** Quantify the extent of overlap between features **Filtering:** Only A features with overlap are reported **Applications:** Overlap statistics, coverage analysis |
--output_bed -bed | boolean_true | Convert BAM input to BED format output. **Usage:** Only applicable when input is BAM format **Effect:** Output genomic coordinates in BED format **Applications:** Converting alignment data to interval format |
--include_header -header | boolean_true | Print the header from the A file prior to results. **Usage:** Preserves metadata and format information from input **Applications:** Maintaining file structure and annotations **Formats:** Particularly relevant for VCF and GFF files |
Performance Options
Name | Type & Properties | Description |
|---|---|---|
--use_split -split | boolean_true | Treat "split" BAM or BED12 entries as distinct BED intervals. **Usage:** Split complex entries into individual intervals **Applications:** Detailed analysis of spliced alignments or multi-part features **Formats:** Applies to BAM alignments and BED12 format |
--sorted_input -sorted | boolean_true | Use the "chromsweep" algorithm for sorted input. **Requirements:** Input must be sorted by chromosome then start coordinate **Performance:** Much faster for large sorted files **Usage:** Optimize processing for pre-sorted genomic data **Sort command:** sort -k1,1 -k2,2n input.bed |
--genome_file -g | file | Genome file to enforce consistent chromosome sort order. **Format:** Tab-delimited file with chromosome names and lengths **Usage:** Only applies when used with -sorted option **Purpose:** Ensure consistent chromosome ordering across input files **Example:** chr1\t249250621 |
--no_name_check -nonamecheck | boolean_true | Don't throw error for different chromosome naming conventions. **Usage:** For sorted data with mixed naming (e.g., "chr1" vs "chr01") **Applications:** Working with data from different sources **Safety:** Allows processing despite naming inconsistencies |
--no_buffer -nobuf | boolean_true | Disable output buffering for real-time processing. **Effect:** Each line printed immediately instead of buffered **Trade-off:** Slower output but enables real-time processing **Applications:** Pipeline integration, streaming analysis |
--input_buffer -iobuf | string | Amount of memory to allocate for input buffer. **Format:** Integer with optional K/M/G suffix **Examples:** "1G", "512M", "2048K" **Usage:** Larger buffers can improve I/O performance for large files **Note:** Currently has no effect with compressed files |
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_subtract/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_subtractbiobox v0.4.0
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