bedtools/bedtools_shift

genomics

intervals

shift

coordinates

offset

flanking

Description

Shift genomic intervals by a specified number of base pairs.

bedtools shift moves genomic intervals (BED/GFF/VCF) by a user-specified number of base pairs.
The tool can shift all features by the same amount, or apply strand-specific shifts to features
on the positive and negative strands separately. Shifts can be absolute values or proportional
to feature length.

This tool is commonly used for:

Adjusting genomic coordinates for analysis offsets
Creating flanking regions around features
Simulating experimental bias or systematic shifts
Generating control regions at specified distances
Converting between different coordinate systems
Modeling positional uncertainty in genomic data

Type

bash_script

License

MIT

Keywords

genomics

intervals

shift

coordinates

offset

flanking

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 v0.4.0 \  
  -main-script target/nextflow/bedtools/bedtools_shift/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file containing genomic intervals to shift. Format: BED, GFF, or VCF file Content: Genomic intervals with coordinates to be shifted Requirements: Must contain valid genomic coordinates Usage: Each interval will be shifted according to specified parameters
--genome -g	file required	Genome file defining chromosome sizes. Format: Tab-delimited text file with chromosome names and sizes Content: Each line contains: <chromName><TAB><chromSize> Usage: Prevents shifted coordinates from exceeding chromosome boundaries Creation: Can be generated with 'samtools faidx' or UCSC Table Browser Example format: chr1 249250621 chr2 243199373

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with shifted genomic intervals. Format: Same format as input file Content: Original intervals with shifted coordinates Boundaries: Coordinates clamped to [0, chromosome_length] range

Name

Type & Properties

--output

file

required

output

Shift Options

Name	Type & Properties	Description
--shift -s	double	Shift all features by this number of base pairs. Usage: Positive values shift downstream, negative values shift upstream Interaction: Cannot be used together with --plus_shift and --minus_shift Percentage mode: When --pct is used, this becomes a fraction (e.g., 0.1 = 10%) Boundary handling: Results clamped to valid chromosome coordinates
--plus_shift -p	double	Shift features on the positive strand by this number of base pairs. Usage: Applied only to features on the + strand Requirement: Must be used together with --minus_shift Interaction: Cannot be used with --shift parameter Percentage mode: When --pct is used, this becomes a fraction
--minus_shift -m	double	Shift features on the negative strand by this number of base pairs. Usage: Applied only to features on the - strand Requirement: Must be used together with --plus_shift Interaction: Cannot be used with --shift parameter Percentage mode: When --pct is used, this becomes a fraction
--percentage -pct	boolean_true	Interpret shift values as fractions of feature length. Effect: Shift distances calculated as fraction × feature_length Example: -s 0.5 shifts each feature by 50% of its length Applications: Proportional shifts, relative positioning Default: false (absolute base pair values)

Name

Type & Properties

--shift

-s

double

--plus_shift

-p

double

--minus_shift

-m

double

--percentage

-pct

boolean_true

Output Options

Name	Type & Properties	Description
--header	boolean_true	Include the original file header in output. Usage: Preserves metadata and format information from input Applications: Maintaining file structure, format compatibility Formats: Particularly useful for VCF and GFF files Default: false (no header included)

Name

Type & Properties

--header

boolean_true