Improvements

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. Please see --help or the documentation on fq2bam for more details.

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

fq2bam 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. Please see --help or the documentation on fq2bam 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.

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)

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'.

Added more sanity checks to handle possible errors in advance.

Grace Hopper (GH200)-specific optimizations.

Default --min-read-length is now 1 base pair to be in line with fq2bam.

Improved error messaging if paired reads have different names.