parabricks

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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.

3installs

Sourcenvidia-bionemo/bionemo-agent-toolkit

Added on2026-08-21

NPX Install

npx skill4agent add nvidia-bionemo/bionemo-agent-toolkit parabricks

SKILL.md Content

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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

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.
Classify the request:
- Runtime → runtime-environment.md
- Tool discovery → tool-index.md
- Specific command → matching
```
references/pbrun-<tool>.md
```
Collect missing biological and filesystem context before generating commands.
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:

bash

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