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

Type

bash_script

License

MIT

Keywords

genomics

bam

annotation

tagging

overlap

alignment

features

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.bam"  
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_tag/main.nf \  
  -params-file params.yaml

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

Name

Type & Properties

--input

-i

file

required

--files

file

required

multiple

--labels

string

multiple

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

Name

Type & Properties

--output

file

required

output

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

Name

Type & Properties

--min_overlap

-f

double

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

Name

Type & Properties

--same_strand

-s

boolean_true

--opposite_strand

-S

boolean_true

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)

Name

Type & Properties

--tag_name

-tag

string

--use_names

-names

boolean_true

--use_scores

-scores

boolean_true

--use_intervals

-intervals

boolean_true