This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling.

For further information visit the rna-fq2bam help page.

Quick Start

# 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:<VERSION-TAG> \
    pbrun rna_fq2bam \
    --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2} \
    --genome-lib-dir /workdir/${PATH_TO_GENOME_LIBRARY}/ \
    --output-dir /outputdir/${PATH_TO_OUTPUT_DIRECTORY} \
    --ref /workdir/${REFERENCE_FILE} \
    --out-bam /outputdir/${OUTPUT_BAM} \
    --read-files-command zcat