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

# 4.0.0-1 Release Notes

Clara Parabricks 4.0.0-1 is a major release with many significant changes. It streamlines how users
get and set up the software and simplifies deployment on different platforms. If you are an existing
Parabricks user, review this section to understand the major changes.

## Licensing Changes

There is no license required to use NVIDIA Parabricks. The container works out of the box once downloaded.

Users who would like Enterprise Support can purchase NVIDIA AI Enterprise licenses, which
provides full-stack support for Parabricks and many other NVIDIA software offerings.

To inquire about Enterprise Support for Parabricks, reach out to the NVIDIA
genomics team at [https://www.nvidia.com/en-gb/clara/genomics/](https://www.nvidia.com/en-gb/clara/genomics/)


## New Tools

Starting with v4.0.0-1 the Clara Parabricks toolset focused primarily on those tools that benefit most from GPU acceleration.

If you would like access to one or more of the tools that are no longer available, contact us
in the [developer forum](https://forums.developer.nvidia.com/c/healthcare/parabricks/290).

### WDL/Nextflow Workflows

Clara Parabricks containers are compatible with WDL and NextFlow for building
customized workflows, intertwining GPU- and CPU-powered tasks with different
compute requirements, and deploying at scale.

These enable workflows to be deployed on cloud batch services as well as local
clusters (e.g. SLURM) in a well managed process, pulling from a combination of
Parabricks and third-party containers and running these on pre-defined
nodes.

![](/clara/parabricks/_files/parabricks-clara.docs.buildwithfern.com/64d520699cb51913ada7fa8f2cc4beb938047eba63a860d16fe6f6f8aa83e5eb/assets/images/Workflow_diagram.png)

For further information on running these workflows, and to see the open-source reference
workflows, which can be easily forked/edited, visit the Clara Parabricks
Workflows repository [https://github.com/clara-parabricks-workflows](https://github.com/clara-parabricks-workflows). This repository
includes recommended instance configurations for deploying the GPU-based tools
on cloud and can be easily forked/edited for your own purposes.

## Improvements

* [deepvariant](/tool-reference/tools/deepvariant) now implements DeepVariant v1.5.

* [haplotypecaller](/tool-reference/tools/haplotypecaller) supports additional original HaplotypeCaller options.

* [deepvariant](/tool-reference/tools/deepvariant) and [deepvariant\_germline](/tool-reference/tools/deepvariant-germline) support the `--channel-insert-size` option.

* [starfusion](/tool-reference/tools/starfusion) now adds `PG:Z:MarkDuplicates` to each output BAM record.

## Bug Fixes

* Corrected rna\_fq2bam sample code. The `--read-files-command zcat`, while not a
  required parameter, is needed for correct operation with compressed FASTQ files.

* Updated the list of supported haplotypecaller options.

* Corrected GATK sample code.

* Fixed an fq2bam bug that occurred when many Ns are present in the fastq files.

* General deepvariant performance improvements.

For further information refer to the [Parabricks datasheet](https://resources.nvidia.com/en-us-hc-genomics/healthcare-genomics#page=1).