bam-to-fastq

name	bam-to-fastq
description	Use when converting BAM alignment files to FASTQ format, including paired-end data requiring separate or interleaved output.
disable-model-invocation	true
user-invocable	true

bam-to-fastq

Quick Start

• Command: bamToFastq -i input.bam -fq reads.fq [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bamToFastq
• Full reference: See references/help.md

When To Use This Tool

• Recover FASTQ from BAM alignments for remapping, QC, or archival export.
• Split paired-end BAM into R1 and R2 FASTQ files with -fq and -fq2.
• Emit a single interleaved FASTQ stream by directing both mates to stdout.
• Reconstruct reads from mate tags with -tags when the BAM carries R2 / Q2 tags.

Common Patterns

# 1) Single-end BAM to FASTQ
bamToFastq \
  -i reads.bam \
  -fq reads.fq

# 2) Paired-end BAM to two FASTQ files
bamToFastq \
  -i reads.qname.bam \
  -fq reads_R1.fq \
  -fq2 reads_R2.fq

# 3) Interleaved paired-end FASTQ
bamToFastq \
  -i reads.qname.bam \
  -fq /dev/stdout \
  -fq2 /dev/stdout > reads.interleaved.fq

Recommended Workflow

1. Decide whether the BAM is single-end, paired-end, or tag-based (-tags) before selecting output mode.
2. For paired-end export, query-name sort or collate the BAM first so mates stay synchronized.
3. Write to fresh FASTQ files and validate mate counts if the output will feed a new aligner.
4. If you need more filtering and flag control, compare against samtools fastq before standardizing the pipeline.

Guardrails

• -i and -fq are required.
• Paired-end export with -fq2 assumes the BAM is grouped or sorted by query name.
• -tags is specialized behavior for BAMs that carry mate sequence / quality in R2 and Q2; it is not a generic paired-end fix.
• The interleaved /dev/stdout pattern is convenient but easy to misuse in shells and pipelines, so redirect carefully.
• Prefer -h for help; the wrapper does not support clean GNU-style --help / --version.