mutectcaller - NVIDIA Docs

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.

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:4.1.0-1 \
    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}

Compatible GATK4 Command

The command below is the GATK4 counterpart of the Parabricks command above. The output from this command will be identical to the output from the above command. See the Output Comparison page for comparing the results.

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            $ gatk Mutect2 \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    --input <INPUT_DIR>/${INPUT_TUMOR_BAM} \
    --tumor-sample tumor \
    --input <INPUT_DIR>/${INPUT_NORMAL_BAM} \
    --normal-sample normal \
    --output <OUTPUT_DIR>/${OUTPUT_VCF}

Mutect2 with Panel of Normals

Parabricks Mutect2 from version 3.7.0-1 has started supporting Panel of Normals to process variants. There are three steps involved:

prepon
running mutectcaller with the index generated by prepon
postpon, updating the vcf with pon information

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            # The first command will generate input.pon that should be done once for the input.vcf.gz
    # 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:4.1.0-1 \
    pbrun prepon --in-pon-file /workdir/${INPUT_PON_VCF}

# Run mutectcaller with the pon index
    # 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:4.1.0-1 \
    pbrun mutectcaller \
    --ref /workdir/${REFERENCE_FILE} \
    --tumor-name tumor \
    --in-tumor-bam /workdir/${INPUT_TUMOR_BAM} \
    --in-normal-bam /workdir/${INPUT_NORMAL_BAM} \
    --pon /workdir/${INPUT_PON_VCF} \
    --normal-name normal \
    --out-vcf /outputdir/${OUTPUT_VCF}

# Add the annotation to the output.vcf generated above
    # 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:4.1.0-1 \
    pbrun postpon \
  --in-vcf /workdir/${OUTPUT_VCF} \
  --in-pon-file /workdir/${INPUT_PON_FILE} \
  --out-vcf /outputdir/${OUTPUT_ANNOTATED_VCF}

mutectcaller Reference

Run GPU mutect2 to convert BAM/CRAM to vcf

Input/Output file options

--ref REF
--out-vcf OUT_VCF
--in-tumor-bam IN_TUMOR_BAM
--in-normal-bam IN_NORMAL_BAM
--in-tumor-recal-file IN_TUMOR_RECAL_FILE
--in-normal-recal-file IN_NORMAL_RECAL_FILE
--interval-file INTERVAL_FILE
--pon PON

Tool Options:

--ploidy PLOIDY
--max-mnp-distance MAX_MNP_DISTANCE
--mutectcaller-options MUTECTCALLER_OPTIONS
--tumor-name TUMOR_NAME
--normal-name NORMAL_NAME
-L INTERVAL, --interval INTERVAL
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING

Common options:

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

GPU options:

--num-gpus NUM_GPUS