> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/v4.7.1/about-parabricks/software-overview/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server.

# Software Overview

Parabricks supports the following tools:

![](/clara/parabricks/_fern-img/78c120707198cc1b196b8b2cce498acfee9255a278a1eda8a81ec56d0f798e6f.webp)

---

The [somatic (Somatic Variant Caller)](/tool-reference/tools/somatic), [germline (GATK Germline Pipeline)](/tool-reference/tools/germline), [pacbio_germline](/tool-reference/tools/pacbio_germline),
[ont_germline](/tool-reference/tools/ont_germline), [deepvariant_germline](/tool-reference/tools/deepvariant_germline) and [pangenome_germline](/tool-reference/tools/pangenome_germline)
tools are a collection of several individual tools that are frequently run together,
each grouped as a single command for the users convenience. For example, [deepvariant_germline](/tool-reference/tools/deepvariant_germline)
takes FASTA and FASTQ files as input and produces a VCF and BAM file as output.
Internally, it runs BWA-MEM alignment, performs coordinate sorting, marks duplicates,
and then runs DeepVariant.

Refer to the [Tool Reference](/tool-reference) for lists of all the individual tools. Refer to
[Parabricks WDL/Nextflow Workflows](/about-parabricks/software-overview/nvidia-parabricks-wdl-nextflow-workflows) for information on using Parabricks
with WDL and Nextflow. The [Output Accuracy and Compatible CPU Software Versions](/about-parabricks/software-overview/output-accuracy-and-compatible-cpu-software-versions) page lists the
open-source CPU tools Parabricks is compatible with.

## Docs

- [Software Tools](https://docs.nvidia.com/clara/parabricks/v4.7.1/about-parabricks/software-overview/software-tools.md): 
- [NVIDIA Parabricks WDL/Nextflow Workflows](https://docs.nvidia.com/clara/parabricks/v4.7.1/about-parabricks/software-overview/nvidia-parabricks-wdl-nextflow-workflows.md): 
- [Output Accuracy and Compatible CPU Software Versions](https://docs.nvidia.com/clara/parabricks/v4.7.1/about-parabricks/software-overview/output-accuracy-and-compatible-cpu-software-versions.md):