mutectcaller - NVIDIA Docs

GPU accelerated mutect2. mutectcaller supports tumor or tumor-normal variant calling. 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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            $ pbrun mutectcaller \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --tumor-name tumor \
    --in-tumor-bam tumor.bam \
    --in-normal-bam normal.bam \
    --normal-name normal \
    --out-vcf 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 Ref/Homo_sapiens_assembly38.fasta \
    --input tumor.bam \
    --tumor-sample tumor \
    --input normal.bam \
    --normal-sample normal \
    --output 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
$ pbrun prepon --in-pon-file input.vcf.gz

#Run mutectcaller with the pon index
$ pbrun mutectcaller \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --tumor-name tumor \
    --in-tumor-bam tumor.bam \
    --in-normal-bam normal.bam \
    --pon input.vcf.gz \
    --normal-name normal \
    --out-vcf output.vcf

#Add the annotation to the output.vcf generated above
$ pbrun postpon \
  --in-vcf output.vcf \
  --in-pon-file input.vcf.gz
  --out-vcf 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

Options specific to this tool

--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
--license-file LICENSE_FILE
--no-seccomp-override
--version

GPU options:

--num-gpus NUM_GPUS
--gpu-devices GPU_DEVICES