bed12-to-bed6

name	bed12-to-bed6
description	Use when you need to explode BED12 transcript or block annotations into one BED6 interval per block, such as converting multi-exon records into simple exon intervals for downstream interval analysis.
disable-model-invocation	true
user-invocable	true

bed12-to-bed6

Quick Start

• Command: bed12ToBed6 -i transcripts.bed12 [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bed12ToBed6
• Full reference: See references/help.md

When To Use This Tool

• Split BED12 transcript or gene models into one BED6 record per block.
• Convert exon-style annotations into simple intervals for downstream intersect, coverage, or map workflows.
• Preserve block order in the score column with -n when downstream code needs exon numbering.
• Simplify BED12 inputs before using tools that only expect BED3/BED6-style intervals.

Common Patterns

# 1) Expand BED12 transcripts into BED6 exon intervals
bed12ToBed6 \
  -i transcripts.bed12 \
  > exons.bed

# 2) Write the 1-based block number into the BED score column
bed12ToBed6 \
  -i transcripts.bed12 \
  -n \
  > exons-numbered.bed

Recommended Workflow

1. Confirm the input is true BED12 with consistent blockCount, blockSizes, and blockStarts fields.
2. Decide whether the BED score should stay as the original score or be overwritten with the 1-based block number via -n.
3. Run the conversion and redirect to a new BED6 file for downstream interval work.
4. Spot-check that the output record count matches the total number of blocks you expected from the source annotation.

Guardrails

• Each BED12 block becomes its own BED6 record; the original block arrays are consumed and not carried forward.
• -n overwrites the BED score field, so do not use it if the original score must be preserved.
• Invalid BED12 rows can silently produce misleading output; validate block counts and array lengths upstream.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before showing usage text.