Release v1.6.3

Sentieon Pangenome

• Update the behavior of the --gvcf argument so that both gVCF and VCF files are generated
• Add support for custom extract models (for non-hg38 reference genomes)

Release v1.6.2

General updates

• The sentieon-cli is now available on PyPI, https://pypi.org/project/sentieon_cli/
• Container images are now automatically pushed to DockerHub, https://hub.docker.com/r/sentieon/sentieon-cli
• Add a dependency on Sentieon's vcflib and replace sentieon pyexec with sys.executable
• Improve pipeline input validation
• Improve error reporting during input validation
• Updates and improvements to the Dockerfile

Sentieon Pangenome

• Improve runtime with BAM/CRAM input through replacement of samtools merge with Sentieon's ReadWriter
• Improve sharded error reporting
• Additional functionality
  • Ploidy and sex estimation
  • STR expansion detection with ExpansionHunter
  • HLA and KIR typing with t1k
  • Handling of medically relevant genes inside of large segmental duplications with segdup-caller

Release v1.6.1

General updates

• Rename the sentieon-pangenome pipeline to dnascope-pangenome
• Remove the old pangenome pipeline.

Release v1.6.0

General updates

• General improvements
• Support Python 3.14 and update minimum Python version to 3.11
• Remove the colorlog and importlib_resources dependencies

DNAscope LongRead

• Fix an error during haploid merging

Sentieon Pangenome

• Add support for gVCF output
• Add support for pangenome-informed SV and CNV calling

Release v1.5.2

DNAscope LongRead

• Add support for population vcf input
• Fix a bug where RepeatModel output was not used correctly

Release v1.5.1

General updates

• Add a --version argument

DNAscope Hybrid

• Add support for population vcf input

Pangenome

• Check that the kmc executable supports reading from stdin

Release v1.5.0

General updates

• Use exec instead of the shell to run commands
• Update the bcftools dependency of most pipelines to v1.22, which allows for simultaneous vcf generation and indexing.
• Update the packaging version.

Pangenome

• Introduce a new pipeline, sentieon-pangenome for accelerated alignment to the pangenome graph. This pipeline replaces the earlier pangenome pipeline with vg giraffe alignment.

DNAscope LongRead

• Updates to vcf_mod.py to fix the RPA annotation.
• Add -L to minimap2 commands to handle alignments with very long CIGAR strings.

DNAscope Hybrid

• With --rgsm, completely replace readgroups during variant calling.

Release v1.4.0

General updates

• Terminate running jobs gracefully after receiving a catchable exception (SIGINT and SIGTERM)

Pangenome

Initial alpha/beta implementation of a pangenome alignment and variant calling pipeline. The pangenome pipeline uses vg giraffe for alignment to the pangenome and DNAscope for small variant calling. Please review the pipeline documentation for more information.

Release v1.3.0

General updates

• Add unit and integration tests.
• Simplify the command-line help by hiding some rarely used arguments.
• Add a workaround if lscpu is not available.

DNAscope Hybrid

• Remove the TrimRepeat argument in the hybrid ONT pipeline.
• Require an ONT bundle version > 1.2. Earlier versions of the ONT bundle are trained using the TrimRepeat argument.

Release v1.2.3

General updates

• Refactor all pipelines, removing the external dependency on argh.
• Updates to the test pipelines.

DNAscope Hybrid

• Ensure that readgroups information is passed correctly between functions, fixing a bug in the alignment and variant calling pipeline.