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 with the new reference genome.

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

For further information visit the bam2fq help page.

Quick Start

An example bam2fq command:

#This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks-bam2fq:<VERSION-TAG> \
    pbrun bam2fq \
    --in-bam /workdir/${INPUT_BAM} \
    --out-fq1 /outputdir/${OUTPUT_FASTQ_1}  \
    --out-fq2 /outputdir/${OUTPUT_FASTQ_2}