bedpe-to-bam

name	bedpe-to-bam
description	Use when converting BEDPE (or BED/GFF/VCF) feature records to BAM format for downstream analysis.
disable-model-invocation	true
user-invocable	true

bedpe-to-bam

Quick Start

• Command: bedpeToBam -i pairs.bedpe -g genome.txt [options] > output.bam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bedpeToBam
• Full reference: See references/help.md

When To Use This Tool

• Convert paired-end interval records into BAM-like output.
• Represent pair geometry in BAM for downstream visualization or tooling compatibility.
• Assign a consistent mapping-quality field to synthetic BAM records.
• Produce uncompressed BAM output when piping directly into other tools.

Common Patterns

# 1) Convert BEDPE to BAM
bedpeToBam \
  -i pairs.bedpe \
  -g genome.txt > pairs.bam

# 2) Set a custom mapping quality
bedpeToBam \
  -i pairs.bedpe \
  -g genome.txt \
  -mapq 60 > pairs.mapq60.bam

# 3) Stream uncompressed BAM
bedpeToBam \
  -i pairs.bedpe \
  -g genome.txt \
  -ubam > pairs.ubam

Recommended Workflow

1. Confirm the input really represents paired features and that the genome file matches its coordinate system.
2. Use a clear mapping-quality policy if the BAM will be consumed by tools that inspect MAPQ.
3. Emit the BAM, then inspect a few records with samtools view or a browser.
4. Keep this as a format-conversion step rather than a substitute for real aligner-produced BAM when alignment semantics matter.

Guardrails

• -i and -g are required.
• The help text is sparse; verify the exact input schema you are converting before trusting the resulting BAM semantics.
• Default mapping quality is 255, which is a placeholder-like value rather than an inferred alignment score.
• -ubam changes the output stream format but not the record semantics.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.