# Parabricks > Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows. Do NOT use for inspecting or accelerating whole pipelines — use genomics-workflow-acceleration. - Skill: `nvidia-bionemo/parabricks` (Agent Skill, multi-file: 37 files) - Install (CLI): `npx skillmds@latest add nvidia-bionemo/parabricks` - Raw SKILL.md: https://api.skillmd.com/api/skills/nvidia-bionemo/parabricks/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Productivity - License: CC-BY-4.0 AND Apache-2.0 - Author: nvidia-bionemo (https://skillmd.com/u/nvidia-bionemo) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/nvidia-bionemo/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](references/tool-index.md) first, then load the matching `references/pbrun-.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](references/runtime-environment.md) - **Tool discovery** → [tool-index.md](references/tool-index.md) - **Specific command** → matching `references/pbrun-.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](references/pbrun-applybqsr.md) | Apply BQSR table to aligned BAM | | `bam2fq` | [pbrun-bam2fq.md](references/pbrun-bam2fq.md) | BAM → FASTQ conversion | | `bamsort` | [pbrun-bamsort.md](references/pbrun-bamsort.md) | Standalone BAM sort | | `bqsr` | [pbrun-bqsr.md](references/pbrun-bqsr.md) | Generate BQSR recalibration table | | `fq2bam` | [pbrun-fq2bam.md](references/pbrun-fq2bam.md) | Short-read DNA paired FASTQ → BAM/CRAM | | `fq2bam_meth` | [pbrun-fq2bam_meth.md](references/pbrun-fq2bam_meth.md) | Bisulfite/methylation FASTQ → BAM/CRAM | | `giraffe` | [pbrun-giraffe.md](references/pbrun-giraffe.md) | Pangenome graph alignment | | `markdup` | [pbrun-markdup.md](references/pbrun-markdup.md) | Standalone duplicate marking | | `minimap2` | [pbrun-minimap2.md](references/pbrun-minimap2.md) | Long-read FASTQ alignment | | `rna_fq2bam` | [pbrun-rna_fq2bam.md](references/pbrun-rna_fq2bam.md) | RNA-seq FASTQ(s) → splice-aware BAM (STAR alignment) | | `starfusion` | [pbrun-starfusion.md](references/pbrun-starfusion.md) | Fusion detection from chimeric junction input + STAR-Fusion genome library | | `germline` | [pbrun-germline.md](references/pbrun-germline.md) | GATK-style germline pipeline from FASTQ | | `deepvariant_germline` | [pbrun-deepvariant_germline.md](references/pbrun-deepvariant_germline.md) | DeepVariant germline pipeline from FASTQ | | `haplotypecaller` | [pbrun-haplotypecaller.md](references/pbrun-haplotypecaller.md) | Standalone HaplotypeCaller from BAM/CRAM | | `deepvariant` | [pbrun-deepvariant.md](references/pbrun-deepvariant.md) | Standalone DeepVariant from BAM/CRAM | | `somatic` | [pbrun-somatic.md](references/pbrun-somatic.md) | Tumor-normal somatic pipeline | | `mutectcaller` | [pbrun-mutectcaller.md](references/pbrun-mutectcaller.md) | Mutect2-compatible somatic calling | | `deepsomatic` | [pbrun-deepsomatic.md](references/pbrun-deepsomatic.md) | DeepSomatic-based somatic calling | | `pacbio_germline` | [pbrun-pacbio_germline.md](references/pbrun-pacbio_germline.md) | PacBio long-read germline | | `ont_germline` | [pbrun-ont_germline.md](references/pbrun-ont_germline.md) | Oxford Nanopore long-read germline | | `pangenome_germline` | [pbrun-pangenome_germline.md](references/pbrun-pangenome_germline.md) | Pangenome-aware germline | | `pangenome_aware_deepvariant` | [pbrun-pangenome_aware_deepvariant.md](references/pbrun-pangenome_aware_deepvariant.md) | Pangenome-aware DeepVariant | | `prepon` | [pbrun-prepon.md](references/pbrun-prepon.md) | Pangenome-aware preprocessing | | `postpon` | [pbrun-postpon.md](references/pbrun-postpon.md) | Pangenome-aware post-processing | | `bammetrics` | [pbrun-bammetrics.md](references/pbrun-bammetrics.md) | Whole-genome coverage/depth metrics | | `collectmultiplemetrics` | [pbrun-collectmultiplemetrics.md](references/pbrun-collectmultiplemetrics.md) | Multiple Picard/GATK-style alignment metrics | | `genotypegvcf` | [pbrun-genotypegvcf.md](references/pbrun-genotypegvcf.md) | Joint-genotype GVCF input(s) into VCF | | `indexgvcf` | [pbrun-indexgvcf.md](references/pbrun-indexgvcf.md) | Index GVCF input | | `dbsnp` | [pbrun-dbsnp.md](references/pbrun-dbsnp.md) | dbSNP annotation on variant files | For routing heuristics when multiple tools could apply, see [tool-index.md](references/tool-index.md). ## Runtime Readiness For GPU, driver, Docker, container, storage, or installation questions, read [runtime-environment.md](references/runtime-environment.md) and prefer: ```bash python3 skills/parabricks/scripts/check_parabricks_runtime.py ``` Add `--path ` for known input/output/tmp paths. Run container probes only with user consent. ## Command Shape ```bash docker run --rm --gpus all \ --volume /host/input:/workdir \ --volume /host/output:/outputdir \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks: \ pbrun \ ``` 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: - Output accuracy and compatible CPU software versions: - Getting started: - Overview: