shift-bed

name	shift-bed
description	Use when you need to shift genomic intervals in BED/GFF/VCF files by a specified number of base pairs, either uniformly or strand-specifically.
disable-model-invocation	true
user-invocable	true

shift-bed

Quick Start

• Command: shiftBed -i <bed/gff/vcf> -g <genome> -s <int>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/shiftBed
• Full reference: See references/help.md

When To Use This Tool

• Translate intervals left or right along the genome by a fixed distance.
• Shift plus- and minus-strand features by different amounts with -p and -m.
• Express shifts as a fraction of feature length with -pct.
• Create offset control regions or adjust reported interval centers while preserving interval width.

Common Patterns

# 1) Shift every interval 100 bp
shiftBed \
  -i peaks.bed \
  -g genome.sizes \
  -s 100

# 2) Shift plus and minus strands in opposite directions
shiftBed \
  -i transcripts.bed \
  -g genome.sizes \
  -p 500 \
  -m -500

# 3) Shift by 10% of each feature length
shiftBed \
  -i intervals.bed \
  -g genome.sizes \
  -s 0.10 \
  -pct

Recommended Workflow

1. Prepare a genome file (or FASTA .fai) so bedtools can clamp shifted features to chromosome bounds.
2. Decide whether the shift is uniform with -s or strand-specific with -p and -m.
3. Decide whether values are absolute base pairs or fractions of feature length via -pct.
4. Inspect the output for boundary clipping at chromosome starts and ends before using it in downstream analysis.

Guardrails

• -i and -g are both required.
• Use either -s alone or -p together with -m; those modes are mutually exclusive.
• With -pct, values like 0.10 mean 10% of feature length, not 0.10 bp.
• Starts are clipped to 0 and ends are clipped to chromosome length when a shift would move a feature out of bounds.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.