> 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.

# 4.2.0-1 Release Notes

Several packages have been updated to GATK 4.3.  Support for read lengths of up
to 500 base pairs has been added to [haplotypecaller](/tool-reference/tools/haplotypecaller) and
[mutectcaller](/tool-reference/tools/mutectcaller).

Several performance improvements.

A number of bugs have been fixed.

Added [markdup](/tool-reference/tools/markdup), a tool to locate and tag duplicate reads in a BAM or SAM file, where duplicate
reads are defined as originating from a single fragment of DNA.

## Improvements

[deepvariant](/tool-reference/tools/deepvariant):

* Major performance improvements.

[collectmultiplemetrics](/tool-reference/tools/collectmultiplemetrics):

* Supports read lengths of up to 500 base pairs.

[haplotypecaller](/tool-reference/tools/haplotypecaller):

* Updated to GATK 4.3.
* Supports read lengths of up to 500 base pairs.
* Adds support for the `--htvc-bam-output` option.
* `--batch` is deprecated.

[mutectcaller](/tool-reference/tools/mutectcaller):

* Updated to GATK 4.3.
* Supports read lengths of up to 500 base pairs.
* Adds support for the `--run-partition` option.

[bammetrics](/tool-reference/tools/bammetrics)

* Updated to GATK 4.3.

[bqsr](/tool-reference/tools/bqsr)

* Clarified error messages.

### Improvements Spanning Multiple Tools

* Added more error checking when writing BAM files using `--gpuwrite`.
* Improved performance for BWA alignment, particularly for reads > 250 bases in length.
* Added [GPUDirect Storage (GDS)](https://docs.nvidia.com/gpudirect-storage/index.html) support for [fq2bam (BWA-MEM + GATK)](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) and associated pipelines.
* Added a low memory mode for `--gpuwrite` (affects sorting).

## Bug Fixes

* [deepvariant](/tool-reference/tools/deepvariant) Could only handle 32 alt alleles per candidate; can now handle up to 64.
* [bamsort](/tool-reference/tools/bamsort) Bamsort could fail for certain coordinate sorts.

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