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