parabricks

Parabricks

Purpose

Use this skill to discover the right NVIDIA Parabricks pbrun command, assess runtime readiness, and generate version-aware command guidance for individual tools and pipelines.

Do not use this skill for whole-workflow inspection, acceleration planning, or wiring optional GPU branches. For pipeline-level work, use genomics-workflow-acceleration.

When to Use This Skill

• Which pbrun tool fits the user's data and goal
• GPU, driver, Docker, container, storage, or installation readiness
• Command shape, flags, and validation for a specific Parabricks tool
• Troubleshooting a single Parabricks command or tool family

Prerequisites

Ask for input data type, sequencing technology, reference build, sample structure, desired output, target Parabricks version/container tag, and runtime target before recommending commands.

If the user is unsure which tool applies, read tool-index.md first, then load the matching references/pbrun-<tool>.md file.

Limitations

This skill routes and guides Parabricks commands. It does not install Parabricks, infer missing sample metadata, guarantee output parity, provide clinical interpretation, or promise exact runtime without benchmark data.

Workflow

1. Confirm the Parabricks version or container tag. Verify the current NVIDIA docs when the user asks for the latest tool list or version-sensitive flags.
2. Classify the request:
   • Runtime → runtime-environment.md
   • Tool discovery → tool-index.md
   • Specific command → matching references/pbrun-<tool>.md
3. Collect missing biological and filesystem context before generating commands.
4. Generate conservative Docker commands with explicit mounts, workdir, and placeholders. Validate paths, indexes, and outputs after command generation.

Tool Reference Index

Load only the reference file for the selected tool.

Tool	Reference	Use when
applybqsr	pbrun-applybqsr.md	Apply BQSR table to aligned BAM
bam2fq	pbrun-bam2fq.md	BAM → FASTQ conversion
bamsort	pbrun-bamsort.md	Standalone BAM sort
bqsr	pbrun-bqsr.md	Generate BQSR recalibration table
fq2bam	pbrun-fq2bam.md	Short-read DNA paired FASTQ → BAM/CRAM
fq2bam_meth	pbrun-fq2bam_meth.md	Bisulfite/methylation FASTQ → BAM/CRAM
giraffe	pbrun-giraffe.md	Pangenome graph alignment
markdup	pbrun-markdup.md	Standalone duplicate marking
minimap2	pbrun-minimap2.md	Long-read FASTQ alignment
rna_fq2bam	pbrun-rna_fq2bam.md	RNA-seq FASTQ(s) → splice-aware BAM (STAR alignment)
starfusion	pbrun-starfusion.md	Fusion detection from chimeric junction input + STAR-Fusion genome library
germline	pbrun-germline.md	GATK-style germline pipeline from FASTQ
deepvariant_germline	pbrun-deepvariant_germline.md	DeepVariant germline pipeline from FASTQ
haplotypecaller	pbrun-haplotypecaller.md	Standalone HaplotypeCaller from BAM/CRAM
deepvariant	pbrun-deepvariant.md	Standalone DeepVariant from BAM/CRAM
somatic	pbrun-somatic.md	Tumor-normal somatic pipeline
mutectcaller	pbrun-mutectcaller.md	Mutect2-compatible somatic calling
deepsomatic	pbrun-deepsomatic.md	DeepSomatic-based somatic calling
pacbio_germline	pbrun-pacbio_germline.md	PacBio long-read germline
ont_germline	pbrun-ont_germline.md	Oxford Nanopore long-read germline
pangenome_germline	pbrun-pangenome_germline.md	Pangenome-aware germline
pangenome_aware_deepvariant	pbrun-pangenome_aware_deepvariant.md	Pangenome-aware DeepVariant
prepon	pbrun-prepon.md	Pangenome-aware preprocessing
postpon	pbrun-postpon.md	Pangenome-aware post-processing
bammetrics	pbrun-bammetrics.md	Whole-genome coverage/depth metrics
collectmultiplemetrics	pbrun-collectmultiplemetrics.md	Multiple Picard/GATK-style alignment metrics
genotypegvcf	pbrun-genotypegvcf.md	Joint-genotype GVCF input(s) into VCF
indexgvcf	pbrun-indexgvcf.md	Index GVCF input
dbsnp	pbrun-dbsnp.md	dbSNP annotation on variant files

For routing heuristics when multiple tools could apply, see tool-index.md.

Runtime Readiness

For GPU, driver, Docker, container, storage, or installation questions, read runtime-environment.md and prefer:

python3 skills/parabricks/scripts/check_parabricks_runtime.py

Add --path <dir> for known input/output/tmp paths. Run container probes only with user consent.

Command Shape

docker run --rm --gpus all \
  --volume /host/input:/workdir \
  --volume /host/output:/outputdir \
  --workdir /workdir \
  nvcr.io/nvidia/clara/clara-parabricks:<version> \
  pbrun <selected-tool> \
  <tool-specific-options>

Check the version-specific tool reference before finalizing flags.

Troubleshooting

Error	Cause	Solution
Multiple plausible tools	Data type or goal underspecified	Ask for assay, inputs, caller preference, desired output; use tool-index
Exact flag requested	Options are version-sensitive	Check the selected tool reference and NVIDIA docs
Runtime question	GPU, Docker, drivers, or storage	Use runtime-environment reference and diagnostic script
Wrong tool family	Assay or input type unclear	Confirm DNA/RNA/methylation/long-read/pangenome before routing
CUDA or memory failure	Runtime not ready or GPU memory constrained	Assess runtime before tuning command flags

Guardrails

• Treat command availability and options as version-sensitive.
• Do not infer exact flags from command names alone.
• Do not collapse standalone tools and full pipelines when explaining tradeoffs.
• Do not substitute DNA fq2bam for RNA, or germline for somatic callers.
• Do not invent sample names, read groups, reference builds, known-sites files, model files, graph resources, container tags, or output paths.
• Do not install, upgrade, or modify packages. Label setup commands as user-run.
• Do not claim CPU execution of Parabricks tools.
• Do not claim biological or VCF parity without a comparison run.
• Prefer official NVIDIA docs for exact command syntax and option defaults.

Key References

• Parabricks tool index: https://docs.nvidia.com/clara/parabricks/latest/toolreference.html
• Output accuracy and compatible CPU software versions: https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/outputaccuracyandcompatiblecpusoftwareversions.html
• Getting started: https://docs.nvidia.com/clara/parabricks/latest/gettingstarted.html
• Overview: https://docs.nvidia.com/clara/parabricks/latest/overview.html