This tool is an accelerated version of the GATK somatic variant caller, Mutect2, which takes aligned BAMs from the FQ2BAM tool, and outputs a VCF file. This can take as input either a single (“tumor-only”) BAM, or a pair of BAMs (“tumor-normal”) to provide a baseline to call somatic variants against.

The figure below shows the high-level functionality of mutectcaller. All dotted boxes indicate optional data, with some constraints.

For further information visit the mutectcaller 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 mutectcaller \
    --ref /workdir/${REFERENCE_FILE} \
    --tumor-name tumor \
    --in-tumor-bam /workdir/${INPUT_TUMOR_BAM} \
    --in-normal-bam /workdir/${INPUT_NORMAL_BAM} \
    --normal-name normal \
    --out-vcf /outputdir/${OUTPUT_VCF}