bedtools/bedtools_fisher
genomics
intervals
fisher
statistics
overlap
significance
test
Description
Calculate Fisher's exact test statistic between two feature files.
This tool performs Fisher's exact test to assess the statistical significance
of overlaps between genomic intervals in two files. It calculates the probability
of observing the given overlap pattern by chance, providing a p-value for
statistical inference.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input_a -a | file required | First input file for comparison. **Format:** BED, GFF, VCF file with genomic intervals **Requirement:** Must be sorted by chromosome, then start position **Usage:** File A for Fisher's exact test comparison |
--input_b -b | file required | Second input file for comparison. **Format:** BED, GFF, VCF file with genomic intervals **Requirement:** Must be sorted by chromosome, then start position **Usage:** File B for Fisher's exact test comparison |
--genome -g | file required | Genome file defining chromosome sizes. **Format:** Tab-delimited file with chromosome name and size **Purpose:** Enforces consistent chromosome sort order **Example:** chr1\t249250621 |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file with Fisher's exact test results. Contains statistical results including p-values for overlap significance between input files. |
Overlap Options
Name | Type & Properties | Description |
|---|---|---|
--merge_overlaps -m | boolean_true | Merge overlapping intervals before analysis. **Effect:** Collapses overlapping intervals in both files **Usage:** Prevents double-counting of overlapping features **Default:** false (no merging) |
--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 |
--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 be overlapped |
--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) |
Strand Options
Name | Type & Properties | Description |
|---|---|---|
--same_strand -s | boolean_true | Require same strandedness for overlaps. **Effect:** Only report overlaps on the same strand **Default:** false (strand-independent) |
--opposite_strand -S | boolean_true | Require different strandedness for overlaps. **Effect:** Only report overlaps on opposite strands **Default:** false (strand-independent) |
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 |
Advanced Options
Name | Type & Properties | Description |
|---|---|---|
--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 |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.txt"
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_fisher/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_fisherbiobox v0.4.1
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