parabricks

Compare original and translation side by side

🇺🇸

Original

English

🇨🇳

Translation

Chinese

Parabricks

Purpose

用途

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

使用此技能来找到合适的NVIDIA Parabricks

pbrun

命令，评估运行时就绪性，并为单个工具和流程生成版本适配的命令指导。

请勿将此技能用于完整工作流检查、加速规划或配置可选GPU分支。如需流程级工作，请使用

genomics-workflow-acceleration

。

When to Use This Skill

何时使用此技能

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

哪种
```
pbrun
```
工具适合用户的数据和目标
GPU、驱动程序、Docker、容器、存储或安装就绪性检查
特定Parabricks工具的命令格式、参数和验证
单个Parabricks命令或工具系列的故障排除

Prerequisites

前提条件

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.

在推荐命令前，请询问输入数据类型、测序技术、参考基因组版本、样本结构、期望输出、目标Parabricks版本/容器标签以及运行时目标。

如果用户不确定适用哪种工具，请先阅读tool-index.md，然后加载匹配的

references/pbrun-<tool>.md

文件。

Limitations

限制

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.

此技能仅用于指引和指导Parabricks命令。它不负责安装Parabricks、推断缺失的样本元数据、保证输出一致性、提供临床解读，也不承诺在没有基准数据的情况下给出精确运行时间。

Workflow

工作流程

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.

确认Parabricks版本或容器标签。当用户询问最新工具列表或版本敏感参数时，请查阅当前NVIDIA文档。
对请求进行分类：
- 运行时 → runtime-environment.md
- 工具发现 → tool-index.md
- 特定命令 → 匹配的
```
references/pbrun-<tool>.md
```
在生成命令前收集缺失的生物学和文件系统上下文信息。
生成包含显式挂载、工作目录和占位符的保守Docker命令。命令生成后验证路径、索引和输出。

Tool Reference Index

工具参考索引

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.

仅加载所选工具的参考文件。

工具	参考文档	使用场景
`applybqsr`	pbrun-applybqsr.md	将BQSR表应用于已比对的BAM
`bam2fq`	pbrun-bam2fq.md	BAM → FASTQ格式转换
`bamsort`	pbrun-bamsort.md	独立BAM排序
`bqsr`	pbrun-bqsr.md	生成BQSR校正表
`fq2bam`	pbrun-fq2bam.md	短读长DNA配对FASTQ → BAM/CRAM
`fq2bam_meth`	pbrun-fq2bam_meth.md	亚硫酸氢盐/甲基化FASTQ → BAM/CRAM
`giraffe`	pbrun-giraffe.md	泛基因组比对
`markdup`	pbrun-markdup.md	独立重复标记
`minimap2`	pbrun-minimap2.md	长读长FASTQ比对
`rna_fq2bam`	pbrun-rna_fq2bam.md	RNA-seq FASTQ(s) → 剪接比对BAM（STAR比对）
`starfusion`	pbrun-starfusion.md	基于嵌合 junction输入 + STAR-Fusion基因组文库的融合检测
`germline`	pbrun-germline.md	从FASTQ出发的GATK风格生殖系流程
`deepvariant_germline`	pbrun-deepvariant_germline.md	从FASTQ出发的DeepVariant生殖系流程
`haplotypecaller`	pbrun-haplotypecaller.md	从BAM/CRAM出发的独立HaplotypeCaller
`deepvariant`	pbrun-deepvariant.md	从BAM/CRAM出发的独立DeepVariant
`somatic`	pbrun-somatic.md	肿瘤-正常体细胞流程
`mutectcaller`	pbrun-mutectcaller.md	兼容Mutect2的体细胞变异检测
`deepsomatic`	pbrun-deepsomatic.md	基于DeepSomatic的体细胞变异检测
`pacbio_germline`	pbrun-pacbio_germline.md	PacBio长读长生殖系变异检测
`ont_germline`	pbrun-ont_germline.md	Oxford Nanopore长读长生殖系变异检测
`pangenome_germline`	pbrun-pangenome_germline.md	泛基因组感知的生殖系变异检测
`pangenome_aware_deepvariant`	pbrun-pangenome_aware_deepvariant.md	泛基因组感知的DeepVariant
`prepon`	pbrun-prepon.md	泛基因组感知的预处理
`postpon`	pbrun-postpon.md	泛基因组感知的后处理
`bammetrics`	pbrun-bammetrics.md	全基因组覆盖度/深度统计
`collectmultiplemetrics`	pbrun-collectmultiplemetrics.md	多种Picard/GATK风格的比对统计
`genotypegvcf`	pbrun-genotypegvcf.md	将联合基因型GVCF输入转换为VCF
`indexgvcf`	pbrun-indexgvcf.md	为GVCF输入建立索引
`dbsnp`	pbrun-dbsnp.md	为变异文件添加dbSNP注释

当多个工具都适用时，请参考tool-index.md中的路由规则。

Runtime Readiness

运行时就绪性

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.

对于GPU、驱动程序、Docker、容器、存储或安装相关问题，请阅读runtime-environment.md，并优先使用：

bash

python3 skills/parabricks/scripts/check_parabricks_runtime.py

如需指定已知的输入/输出/临时路径，请添加

--path <dir>

。仅在用户同意的情况下运行容器探测。

Command Shape

命令格式

bash

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.

bash

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>

在确定参数前，请查阅版本对应的工具参考文档。

Troubleshooting

故障排除

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

错误	原因	解决方案
多个工具看似适用	数据类型或目标未明确	询问检测类型、输入数据、变异检测工具偏好、期望输出；使用工具索引
请求精确参数	参数因版本而异	查阅所选工具的参考文档和NVIDIA官方文档
运行时问题	GPU、Docker、驱动程序或存储问题	使用运行时环境参考文档和诊断脚本
工具系列选择错误	检测类型或输入数据不明确	在指引前确认是DNA/RNA/甲基化/长读长/泛基因组数据
CUDA或内存错误	运行时未就绪或GPU内存不足	在调整命令参数前评估运行时状态

Guardrails

约束规则

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.

命令可用性和参数因版本而异，请予以重视。
请勿仅根据命令名称推断精确参数。
在解释权衡时，请勿混淆独立工具和完整流程。
请勿用DNA的
```
fq2bam
```
替代RNA工具，或用生殖系工具替代体细胞变异检测工具。
请勿编造样本名称、读取组、参考基因组版本、已知位点文件、模型文件、图谱资源、容器标签或输出路径。
请勿安装、升级或修改软件包。将设置命令标记为需用户自行运行。
请勿声称Parabricks工具可在CPU上运行。
请勿在未进行对比运行的情况下声称生物学或VCF输出一致性。
精确的命令语法和参数默认值请优先参考NVIDIA官方文档。

Key References

关键参考

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

Parabricks工具索引： https://docs.nvidia.com/clara/parabricks/latest/toolreference.html
输出准确性和兼容CPU软件版本： https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/outputaccuracyandcompatiblecpusoftwareversions.html
快速入门： https://docs.nvidia.com/clara/parabricks/latest/gettingstarted.html
概述： https://docs.nvidia.com/clara/parabricks/latest/overview.html