Improvements

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

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

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

Improvements to both the progress meter and error logging messages.

Support for additional arguments with the fq2bam sorting step: --gpusort, --gpuwrite, --gpuwrite-deflate-algo, --use-gds, and more.