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# 4.2.1-1 Release Notes

Two new beta tools have been released: fq2bamfast
and [minimap2](/tool-reference/tools/minimap-2).

A new beta pipeline has been released: [pacbio\_germline](/tool-reference/tools/pacbio-germline).

Performance improvements include fq2bamfast,
a faster version of the
existing [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) and the ability to run the variant caller in [germline](/tool-reference/tools/germline-gatk-germline-pipeline) and
[deepvariant\_germline](/tool-reference/tools/deepvariant-germline) in parallel with BAM generation.

A number of bugs have been fixed.  Most notably, fq2bam read filtering could
have failed with read sizes more than \~500 basepairs.

## New Tools

With this release we have added two new tools:

* fq2bamfast
* [minimap2](/tool-reference/tools/minimap-2)

We have also added one new pipeline:

* [pacbio\_germline](/tool-reference/tools/pacbio-germline)

The new beta fq2bamfast is a re-implementation of
accelerated BWA-MEM present in [fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) to better utilize
GPUs such as A100 and H100.

## Improvements

### Tool Updates

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

* Adds the following new options:

  * `--active-probability-threshold`
  * `--genotype-germline-sites`
  * `--genotype-pon-sites`
  * `--initial-tumor-lod`
  * `--mutect-bam-output`
  * `--pruning-lod-threshold`
  * `--tumor-lod-to-emit`
  * `-max-reads-per-alignment-start` (as part of the `--mutectcaller-options` option)

[fq2bam](/tool-reference/tools/fq-2-bam-bwa-mem-gatk) and associated pipelines: [germline pipeline](/tool-reference/tools/germline-gatk-germline-pipeline), [deepvariant\_pipeline](/tool-reference/tools/deepvariant-germline), and [somatic pipeline](/tool-reference/tools/somatic-somatic-variant-caller):

* New compression options for `--gpuwrite`:
  use `--gpuwrite-deflate-algo 3` for more compression at slightly slower speed
  and `--gpuwrite-deflate-algo 0` for more speed, which continues to be the default.
* Fix edge case with FASTQ filtering.

### Improvements Spanning Multiple Tools

* Added the `--read-from-tmp-dir` option to [germline pipeline](/tool-reference/tools/germline-gatk-germline-pipeline) and [deepvariant\_pipeline](/tool-reference/tools/deepvariant-germline).
  It will run the variant caller in parallel with BAM generation. It has been tested on A100 and H100 but
  might cause out-of-memory on other GPUs.
* Added the `--fq2bamfast` option to [germline pipeline](/tool-reference/tools/germline-gatk-germline-pipeline), [deepvariant\_pipeline](/tool-reference/tools/deepvariant-germline), and
  [somatic pipeline](/tool-reference/tools/somatic-somatic-variant-caller) to use fq2bamfast for alignment.

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