bam-to-bed

name	bam-to-bed
description	Use when converting BAM alignment files to BED6, BED12, or BEDPE format for downstream analysis or visualization.
disable-model-invocation	true
user-invocable	true

bam-to-bed

Quick Start

• Command: bamToBed -i input.bam [options] > output.bed
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bamToBed
• Full reference: See references/help.md

When To Use This Tool

• Convert alignments from BAM into BED6, BED12, or BEDPE for downstream interval analysis.
• Represent split or spliced alignments as separate blocks with -split, -splitD, or -bed12.
• Export paired-end geometry with -bedpe.
• Preserve extra alignment context such as edit distance or CIGAR when BED output alone is too lossy.

Common Patterns

# 1) Basic BAM to BED6
bamToBed \
  -i alignments.bam > alignments.bed

# 2) BED12 output for split alignments
bamToBed \
  -i alignments.bam \
  -bed12 > alignments.bed12

# 3) BEDPE for paired-end reads
bamToBed \
  -i alignments.qname.bam \
  -bedpe > alignments.bedpe

Recommended Workflow

1. Choose the target representation first: BED6 for simple intervals, BED12 for blocked alignments, or BEDPE for read pairs.
2. Query-name sort or group the BAM before using -bedpe.
3. Add -split / -splitD when the CIGAR structure matters for exon-aware or gapped alignments.
4. Redirect stdout to a file and sanity-check coordinates and column count before feeding the result into downstream tools.

Guardrails

• -bedpe requires BAM records to be grouped or sorted by query.
• -bed12 forces -split.
• -splitD also forces -split and breaks on both N and D CIGAR operators.
• -tag must reference a numeric BAM tag and cannot be combined with BEDPE output.
• Default BED score is mapping quality; -ed changes that semantics, especially for BEDPE where the mate edit distances are combined.