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# 4.4.0-1 Release Notes

**Highlights:**

* We are introducing a new tool, the [giraffe](/tool-reference/tools/giraffe-vg-giraffe-gatk) pangenome graph-based aligner for short reads.

  * Read the [How Should I Use giraffe in Parabricks?](/tool-reference/tools/giraffe-vg-giraffe-gatk#how-should-i-use-giraffe-in-parabricks) section in the tool
    reference documentation for advice on getting started and best practices.

* Unified 'multi-architecture' Docker containers for both Grace Hopper and AMD64 architectures.

## New Tools

With Parabricks 4.4.0 we are releasing a GPU-accelerated giraffe tool.
Giraffe is a graph-based short-read mapping tool that efficiently handles genetic diversity and structural variations across populations.
VG Giraffe was originally developed by Dr. Benedict Paten's lab at the
University of California, Santa Cruz (UCSC).

## Improvements

### Tool Updates

Multi-architecture container:

* Instead of pulling different containers for different architectures, you now need
  only pull one container.  The `pull` command will determine which architecture
  is needed.

BAM reader and writer:

* Support for reading and writing BAM records with more than 65535 CIGAR operations.

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

* Support for `--run-partition` in force-calling mode (`--htvc-alleles`).

[rna\_fq2bam](/tool-reference/tools/rna-fq-2-bam):

* Improvements to both the progress meter and error logging messages.
* Support for additional arguments with the [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) sorting step: `--gpusort`, `--gpuwrite`, `--gpuwrite-deflate-algo`, `--use-gds`, and more.

## Bug Fixes

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

* Fixed a crash which occurred if the HG tag value equaled -1 when passing `--mutect-bam-output`.

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

* Fixed a crash which occurred if the HG tag value equaled -1 when passing `--htvc-bam-output`.

[rna\_fq2bam](/tool-reference/tools/rna-fq-2-bam):

* Fixed a crash in the wrapper when passing `--out-sam-unmapped Within_KeepPairs`.

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

* Fixed a deadlock issue that occurred with certain datasets during GPU-accelerated CRAM write operation. (`--gpuwrite`).

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

* Fixed a deadlock issue that occurred with certain datasets during GPU-accelerated CRAM write operation. (`--gpuwrite`).
* Fixed an issue that caused some large reads to not be processed by the fastq reader.

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

* Fixed a crash that occurred in certain edge cases, such as with chromosome MAP2K3\_chr17\_22578583\_22605165, related to handling supported reads.

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