bedtools/bedtools_tag
genomics
bam
annotation
tagging
overlap
alignment
features
Description
Annotate BAM alignments with tags based on overlaps with genomic intervals.
bedtools tag reads alignments from a BAM file and annotates them with custom tags
based on their overlap with intervals from one or more BED/GFF/VCF files. Each
alignment that overlaps with an interval receives a tag in the BAM record, making
this tool essential for marking reads that overlap with specific genomic features
like genes, enhancers, or repetitive elements.
This tool is commonly used for:
Tagging reads that overlap with specific genomic features
Annotating alignments with gene names or functional regions
Marking reads for downstream filtering based on overlap patterns
Quality control by identifying reads in problematic regions
Single-cell RNA-seq analysis for feature assignment
ChIP-seq analysis for peak annotation and read classification
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input BAM file to annotate with tags. **Format:** BAM file with aligned sequencing reads **Content:** Alignments that will be tagged based on overlaps **Requirements:** Must be a valid BAM file (indexed .bai file recommended) **Usage:** Each alignment overlapping with annotation files will receive tags **Output:** Tagged BAM file with additional tag fields |
--files | file required multiple | BED/GFF/VCF annotation files for tagging overlapping alignments. **Format:** BED, GFF, or VCF files with genomic intervals **Content:** Genomic features used for alignment annotation **Usage:** Alignments overlapping these intervals receive tags **Multiple files:** Each file can have its own label for distinction **Requirements:** Files should have consistent chromosome naming with BAM |
--labels | string multiple | Labels corresponding to each annotation file. **Format:** String labels for each annotation file **Usage:** Must provide one label per annotation file in --files **Content:** These labels will be used as tag values in the BAM output **Order:** Must match the order of files in --files parameter **Applications:** Distinguish overlaps from different annotation sources **Note:** Required unless --use_names, --use_scores, or --use_intervals is specified |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output BAM file with tagged alignments. **Format:** BAM file with original alignments plus overlap tags **Content:** All original alignment data plus custom tags for overlaps **Tags:** Alignments overlapping annotation files receive additional tag fields **Preservation:** Non-overlapping alignments remain unchanged **Indexing:** Output can be indexed like any standard BAM file |
Overlap Options
Name | Type & Properties | Description |
|---|---|---|
--min_overlap -f | double | Minimum overlap required as a fraction of the alignment. **Default:** 1E-9 (essentially 1 base pair) **Range:** 0.0 to 1.0 **Usage:** Alignment must overlap at least this fraction of its length **Example:** 0.5 requires alignment to overlap 50% of its length with feature **Applications:** Filter spurious overlaps, require substantial overlap |
Strand Options
Name | Type & Properties | Description |
|---|---|---|
--same_strand -s | boolean_true | Require overlaps on the same strand. **Usage:** Only tag alignments that overlap features on the same strand **Applications:** Strand-specific RNA-seq analysis, sense transcript tagging **Default:** false (overlaps reported without respect to strand) **Interaction:** Mutually exclusive with --opposite_strand |
--opposite_strand -S | boolean_true | Require overlaps on the opposite strand. **Usage:** Only tag alignments that overlap features on the opposite strand **Applications:** Antisense transcript detection, strand-specific filtering **Default:** false (overlaps reported without respect to strand) **Interaction:** Mutually exclusive with --same_strand |
Tag Options
Name | Type & Properties | Description |
|---|---|---|
--tag_name -tag | string | Specify the BAM tag name to use for annotations. **Default:** "YB" **Format:** Two-character string (standard BAM tag format) **Usage:** Custom tag name for storing overlap information **Examples:** "YK", "ZZ", "XG" **Standards:** Follow BAM tag naming conventions |
--use_names -names | boolean_true | Use the name field from annotation files to populate tags. **Usage:** Instead of labels, use the name column from BED/GFF files **Applications:** Gene name tagging, feature-specific annotation **Requirements:** Annotation files must have name fields (4th column in BED) **Default:** false (uses --labels values instead) |
--use_scores -scores | boolean_true | Use the score field from annotation files to populate tags. **Usage:** Instead of labels, use the score column from annotation files **Applications:** Confidence scoring, quantitative tagging **Requirements:** Annotation files must have score fields (5th column in BED) **Default:** false (uses --labels values instead) |
--use_intervals -intervals | boolean_true | Use full interval information to populate tags. **Content:** Include interval coordinates, name, score, and strand in tags **Format:** Full genomic interval description as tag value **Applications:** Detailed annotation tracking, interval provenance **Requirements:** Still requires --labels to identify source files **Default:** false (uses --labels values instead) |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bam"
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_tag/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_tagbiobox v0.4.2
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