How to run Clara Parabricks
Clara Parabricks is a software suite for genomic analysis. It delivers major improvements in throughput time for common analytical tasks in genomics, including germline and somatic analysis. The core of the Parabricks software is its data pipeline, which takes raw data and transforms it according to the user’s requirements.
The Parabricks software supports the tools shown below:
And the pipelines :
The following examples will require using the system console of the GPU host. Click on the “System Console” link in the left menu of this page to open a web-based SSH session.
Those tools are accessible using the Parabricks container. All a user needs to do is run the container using the command line :
docker run --gpus all nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 pbrun <COMMAND>
The first command line we will be running is the one providing help with all the tools and pipelines
<COMMAND> provided by Parabricks
docker run --gpus all --rm \ nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \ pbrun --help Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation usage: pbrun <command> [<args>] Help: pbrun -h command can be a TOOL or FULL PIPELINE. Example: pbrun fq2bam --ref genome.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam sample.bam pbrun germline --ref genome.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam sample.bam --out-variants sample.vcf command options for standalone TOOL fq2bam - Run bwa mem, co-ordinate sorting, marking duplicates and Base Quality Score Recalibration rna_fq2bam - Run RNA-seq data through the fq2bam pipeline bam2fq - Convert a BAM to FASTQ bqsr - Collect BQSR report on a BAM file haplotypecaller - Run GPU-HaplotypeCaller for calling germline variants mutectcaller - Run GPU-Mutect2 for tumor-normal analysis deepvariant - Run GPU-DeepVariant for calling germline variants bammetrics - Collect WGS Metrics on a bam file collectmultiplemetrics - Collect multiple classes of metrics on a bam file applybqsr - Apply BQSR report to a bam file and generate new bam file indexgvcf - Index a GVCF file genotypegvcf - Convert a GVCF to VCF dbsnp - Annotate variants based on a dbsnp prepon - Build an index for pon file, which is the prerequisite to do mutect pon postpon - Generate the final vcf output of doing mutect pon starfusion - Identify candidate fusion transcripts supported by Illumina reads bamsort - Sort BAM file command options for commonly used FULL PIPELINES germline - Run the germline pipeline from FASTQ to VCF deepvariant_germline - Run the germline pipeline from FASTQ to VCF using a deep neural network analysis somatic - Run the somatic pipeline from FASTQ to VCF Information about the software version - Current version of Parabricks Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation positional arguments: command The pipeline or tool to run. optional arguments: -h, --help show this help message and exit