bedtools-genomic-intervals

npx skills add BioTender-max/awesome-bio-agent-skills --skill bedtools-genomic-intervals --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# bedtools — Genomic Interval Analysis Toolkit ## Overview bedtools is the standard toolkit for operating on genomic intervals in BED, BAM, GFF, and VCF formats. It solves the core problem of genome arithmetic: finding overlaps between feature sets, computing coverage, extracting sequences, merging adjacent regions, and annotating features with nearest neighbors. bedtools operates on sorted coordinate lists and runs at C speed, making it practical for whole-genome analyses. ## When to Use - Intersecting ChIP-seq peaks with gene annotations to find promoter-overlapping peaks - Merging overlapping ATAC-seq peaks or called regions across replicates - Computing read coverage depth over target capture regions - Extracting FASTA sequences for motif discovery or primer design - Finding the nearest gene to each regulatory element or variant - Subtracting blacklist or repeat regions from peak calls - Expanding genomic intervals by fixed distance (promoter regions) - Use `tabix` instead for fast indexed queries of a single genomic region - For normalized coverage bigWig tracks, use `deeptools bamCoverage` instead - Use `mosdepth` instead for whole-genome per-base depth (10× faster) ## Prereq

Bioconda (recommended)
conda install -c bioconda bedtools
Homebrew (macOS)
brew install bedtools
Verify
bedtools --version
bedtools v2.31.0
Create genome file from FASTA index
samtools faidx reference.fa
cut -f1,2 reference.fa.fai > genome.txt  # chr → size table