NVIDIA Clara Parabricks Pipelines:Variant Callers: Mutect Caller

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

CLI

$ 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


Options

Option

Description

--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.

--in-normal-bam

Path of bam file for normal reads.

--in-normal- recal-file

Path of BQSR report for normal sample.

--normal-name

Name of sample for normal reads.

--ploidy

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

--interval-file

Path to an interval file for BQSR step with possible formats: Picard-style (.interval_list or .picard), GATK-style (.list or .intervals), or BED file (.bed). This option can be used multiple times (default: None)

--interval(-L)

Interval within which to call variants from the input reads. All intervals will have a padding of 100 to get read records and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times. e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000" (default: None)

--interval-padding(-ip)

Padding size (in base pairs) to add to each interval you are including (default: None)

--tmp-dir

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

--num-gpus

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

--gpu-devices

Which GPU devices to use for a run. By default, all GPU devices will be used. To set specific GPU devices, enter a comma-separated list of GPU device numbers.