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 (FQ2BAM + BWA-MEM) with the new reference genome.

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

Quick Start

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            # 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 \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \
    pbrun bam2fq \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --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. See the Output Comparison page for comparing the results.

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

bam2fq Reference

Run bam2fq to convert BAM/CRAM to FASTQ.

Input/Output file options

--ref REF
--in-bam IN_BAM
--out-prefix OUT_PREFIX

Tool Options:

--out-suffixF OUT_SUFFIXF
--out-suffixF2 OUT_SUFFIXF2
--out-suffixO OUT_SUFFIXO
--out-suffixO2 OUT_SUFFIXO2
--out-suffixS OUT_SUFFIXS
--rg-tag RG_TAG
--remove-qc-failure

Performance Options:

--num-threads NUM_THREADS

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version