# Bed To Igv

> Use when you need to generate an IGV batch script for taking snapshots at loci defined in BED, GFF, or VCF files, especially for repeatable visual review of many regions.

- Skill: `vimalinx/bed-to-igv` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add vimalinx/bed-to-igv`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/bed-to-igv/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/bed-to-igv

---


# bed-to-igv

## Quick Start
- **Command**: `bedToIgv -i loci.bed -path snapshots/ [options] > review.igv.batch`
- **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/bedToIgv`
- **Full reference**: See `references/help.md`

## When To Use This Tool

- Generate repeatable IGV snapshot scripts for a BED / GFF / VCF locus list.
- Automate review of peaks, variants, breakpoints, or candidate loci across many regions.
- Preload an IGV session with `-sess` before snapshotting.
- Standardize snapshot naming, flanking context, read sorting, and collapse settings across a review batch.

## Common Patterns

```bash
# 1) Basic IGV batch script for a BED file
bedToIgv \
  -i loci.bed \
  -path snapshots \
  > loci.igv.batch
```

```bash
# 2) Load a saved IGV session and use the BED name field for filenames
bedToIgv \
  -i peaks.bed \
  -path snapshots \
  -sess tumor-review.xml \
  -name \
  -slop 250 \
  > peaks.igv.batch
```

```bash
# 3) Sort alignments and collapse reads before each image
bedToIgv \
  -i variants.vcf \
  -path snapshots \
  -sort position \
  -clps \
  -img svg \
  > variants.igv.batch
```

## Recommended Workflow

1. Prepare the BED / GFF / VCF interval list and decide whether an existing IGV session should be loaded with `-sess`.
2. Decide where IGV should save the snapshots via `-path`, whether filenames should come from column 4 via `-name`, and whether flanking context is needed with `-slop`.
3. Run `bedToIgv` and redirect stdout into a batch-script file.
4. Open IGV, load the appropriate genome and tracks (or let `-sess` do it), then execute the batch script from within IGV.

## Guardrails

- `-path` sets the snapshot directory used inside IGV; it does not choose where the batch script itself is written.
- The command writes the IGV batch script to stdout, so redirect it to a file explicitly.
- `-name` assumes column 4 is populated with safe, unique names; otherwise the default `chr:start-end.ext` naming is safer.
- The generated script must be run from within IGV, not from the shell.
- Without `-sess`, you must load the correct genome and tracks in IGV before running the script.