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# 4.3.2-1 Release Notes

**Highlights:**

* New pipeline, [ont\_germline](/tool-reference/tools/ont-germline) for long read ONT variant calling.
* [minimap2](/tool-reference/tools/minimap-2) bug fixes and new features.
* Further optimizations and improvements for the [Grace Hopper](/get-started/nvidia-grace-cpu-platforms) architecture.
* Introduced GPU acceleration for CRAM file write operations.

## New Tools

With Parabricks 4.3.2 we are releasing an accelerated ont\_germline pipeline.  The ONT Germline pipeline generates BAM
and variants on long read ONT sequences using minimap2 for alignment as
well as the DeepVariant variant caller.

## Improvements

### Tool Updates

[minimap2](/tool-reference/tools/minimap-2):

* Added new options `--pbmm2` and `--pbmm2-unmapped` that include additional processing to match the output of PacBio's pbmm2.

* Added ability to use unaligned BAM as input instead of FASTQ (`--in-bam`).

* A new higher compression ratio option for BAM/CRAM files with `--gpuwrite`.

* The nvCOMP DEFLATE compression algorithm options have changed for the
  parameter `--gpuwrite-deflate-algo`. See `--help` or
  the documentation on [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) for more details.

* Added GPU acceleration for CRAM write operations (`--gpuwrite`).

[fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk):

* [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) has been surpassed by fq2bamfast: the new
  version of fq2bam with more optimizations for performance. Note that
  fq2bamfast is no longer present as the fq2bam and fq2bamfast tools have
  been merged.

* Added a new option to use a single-ended unaligned BAM as input instead of a FASTQ file (`--in-se-bam`).

* A new higher compression ratio option for BAM/CRAM files with `--gpuwrite`.

* The nvCOMP DEFLATE compression algorithm options have changed for the
  parameter `--gpuwrite-deflate-algo`. See `--help` or
  the documentation on [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) for more details.

* Added GPU acceleration for CRAM write operations (`--gpuwrite`).

* Default `--min-read-length` is 1 base pair; whereas, in fq2bamfast it was 10.

* Improved error messaging if paired reads have different names.

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

* Added a new option `--filter-reads-too-long` to filter out reads with length > 512bp.
* Improved performance and reduced memory consumption when processing long reads (PacBio and ONT data)

[haplotypecaller](/tool-reference/tools/haplotypecaller) added support for:

* Force-calling mode (`--htvc-alleles`).
* The `--min-base-quality-score` argument.
* The `--adaptive-pruning` argument.
* A new annotation `AssemblyComplexity` can be specified by passing `--haplotypecaller-options '-A AssemblyComplexity'`.

[somatic](/tool-reference/tools/somatic-somatic-variant-caller):

* Added more sanity checks to handle possible errors in advance.

[germline pipeline](/tool-reference/tools/germline-gatk-germline-pipeline) and [deepvariant\_germline](/tool-reference/tools/deepvariant-germline):

* Grace Hopper (GH200)-specific optimizations.

[fq2bam\_meth](/tool-reference/tools/fq-2-bam-meth):

* Default `--min-read-length` is now 1 base pair to be in line with [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk).

* Improved error messaging if paired reads have different names.

## Bug Fixes

[minimap2](/tool-reference/tools/minimap-2):

* Fixed a memory leak that was exposed by using a different matching score in the updated preset values.
* Fixed a bug that caused some incorrect SA tag values.
* Fixed a crash caused by `pthread_setaffinity_np`.

[fq2bam (BWA-MEM + GATK)](/tool-reference/tools/fq-2-bam-bwa-mem-gatk):

* Fixed a crash when passing `--bwa-options="-C"` with no comments in the input fastq file(s).

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

* Fixed an invalid GPU memory access in force calling mode (`--mutect-alleles`).
* Fixed additional records in output VCF file when passing `--pon`.

[somatic (Somatic Variant Caller)](/tool-reference/tools/somatic-somatic-variant-caller):

* Fixed a read group ID conflict error in tumor-normal mode when `--tumor-read-group-id-prefix` was not passed from the user.

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

* Fixed an out-of-order issue in the output BAM when passing `--htvc-bam-output`.

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

* Fixed a bug where certain kernels from multiple pipelines (streams) were launched on the default stream.

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