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

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

# 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

# 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.