This tool recalibrates quality scores in a BAM file using the report generated by the bqsr [link] tool. This should be applied after alignment but before variant calling to maximize final accuracy in variant calling, as recommended by GATK best practices. Please note that the applybqsr tool will use at most two GPUs.

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