bam2fq

Run bam2fq to convert BAM/CRAM to FASTQ.

This tool un-aligns a BAM file, reversing it from BAM to FASTQ format. This can be useful if the BAM needs to be re-aligned to a newer or different reference genome by applying bam2fq followed by fq2bam (BWA-MEM + GATK) with the new reference genome.

For paired reads, bam2fq will append “/1” to the 1st read name, and “/2” to the 2nd read name.

Refer to the bam2fq Reference section for a detailed listing of all available options.

Quick Start

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# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
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docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun bam2fq \
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    --ref /workdir/${REFERENCE_FILE} \
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    --in-bam /workdir/${INPUT_BAM} \
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    --out-prefix /workdir/${Prefix_for_output_fastq_files}

Compatible CPU-based BWA-MEM, GATK4 Commands

The command below is the bwa-0.7.15 and GATK4 counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command. Refer to the Output Comparison page for comparing the results.

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$ gatk SamToFastq \
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    -I <INPUT_DIR>/${INPUT_BAM} \
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    -F <OUTPUT_DIR>/${OUTPUT_FASTQ_1} \
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    -F2 <OUTPUT_DIR>/${OUTPUT_FASTQ_2}

Options