This tool generates a Base Quality Score Recalibration report, which can be applied by the applybqsr tool, to recalibrate the quality scores in a BAM file. This is applied as part of the recommended GATK best practices to maximize accuracy in variant calling.

For further information visit the bqsr 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 bqsr \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --knownSites /workdir/${KNOWN_SITES_FILE}
    --out-recal-file /outputdir/${INPUT_RECAL_FILE} \