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