GPU accelerated mutect2

mutectcaller supports tumor or tumor-normal variant calling. The figure below shows high level functionality of mutectcaller. All dotted boxes are optional with some constraints.

Quick Start


$ pbrun mutectcaller --ref Ref/Homo_sapiens_assembly38.fasta \
--in-tumor-bam tumor.bam \
--tumor-name foobar \
--out-vcf output.vcf

Compatible GATK4 command

The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will generate the exact same results as the output from the above command. Please look at Output Comparison page on how you can compare the results.

gatk Mutect2 -R ref.tar.gz --input tumor.bam --tumor-sample foobar --output result.vcf




--ref (required)

The reference genome in fasta format. We assume that the indexing required to run bwa has been completed by the user.

--in-tumor-bam (required)

Path of bam file for tumor reads.

--tumor-name (required)

Name of sample for tumor reads.

--out-vcf (required)

Path to the VCF output file.

--in-tumor- recal-file

Path of BQSR report for tumor sample.


Path of bam file for normal reads.

--in-normal- recal-file

Path of BQSR report for normal sample.


Name of sample for normal reads.


Ploidy assumed for the bam file. Currently only haploid (ploidy 1) and diploid (ploidy 2) are supported.


Defaults to ..
Full path to the directory where temporary files will be stored.


Defaults to number of GPUs in the system.
The number of GPUs to be used for this analysis task.