Tool changes:

• Adds DeepVariant v1.4.0 to both short- and long-read tests

This release is primarily adding two new samples to the PCR-free datasets. The following updates occurred as a result of this change:

• Adds two new samples to our PCR-free datasets corresponding to HG006 and HG007
• PCR-free results all shifted slightly (the vast majority to slightly worse performance); we did not notice any drastic changes across the results; all average sensitivities, precisions, and F1-scores shifted <0.001
• Updates our expected CYP2D6 outputs to include expectations for HG006 and HG007

• Adds dysgu v1.3.10 pass-only to the SV callers for all data types
• Removed full dysgu results from evaluations, pass-only is recommended

• Adds clair3-v0.1-r11 to both Illumina and PacBio test sets; thanks to @zhengzhenxian for assistance and quick TAT while debugging some issues!
• Illumina results shows a slight drop in recall
• PacBio results are borderline identical, but only required ~60% of the compute time compared to r9

• Adds PEPPER-Margin-DeepVariant r0.8
• Removes hg38_GIAB_masked reference, it is recommend to use hg38_T2T_masked instead now

Reference changes:

• Adds the hg38_T2T_masked reference which is version 2 of the hg38_GIAB_masked reference. A brief description and direct download links are provided with the reference metadata.
• The hg38_T2T_masked results tend to be very slightly better than the v1 results, so hg38_GIAB_masked will likely be retired in a future release.

Method changes:

• Truvari was updated to v3.1.0 after the release of a Truvari preprint on bioRxiv. This had a negligible impact on results.

Software changes:

• Updated all other Sentieon-based processes to v202112.01; the vast majority of associated results did not change at all with this update

Software changes:

• Added dnascope-1.0-202112.01-PO for PCR-free datasets, dnascope-0.5-202010.04-PO will be removed in future releases. Additionally, the pass-only filter (e.g. -PO) is recommended for DNAscope, so the unfiltered version has been remove from reporting. Thanks to @DonFreed for the recommendations!
• Added dysgu-1.3.4-PO, which is a pass-only filtered version of dysgu-1.3.4, for PCR-free and PacBio datasets. Additionally, the pass-only filter (e.g. -PO) is recommended for dysgu, so the unfiltered version will be removed in future released. Thanks to @kcleal for the recommendations!

Other changes:

• Added a note in the README on release cadence. In order to reduce overhead, going forward we will limit formal releases to at most once a week. New or partial results may appear through the week with the intention to summarize any changes in the weekly release.

Software changes:

• Adds a temporary sniffles_tr-2.0.2 that incorporates the --tandem-repeats option using the save file as pbsv. This method is shown beside sniffles-2.0.2(no repeat file) for this release to demonstrate the impact of the repeat file on variant calling. It will replace sniffles-2.0.2 in the next release. Thanks to @fritzsedlazeck for the suggestion!

Method change:

• Splits deletion benchmark into RESTRICTED (requiring a high-confidence BED file) and UNRESTRICTED (no BED files, it's everything in the benchmark VCF)
• RESTRICTED now only contains HG002 with the Tier1 regions. This set is more fair when judging the precision of the aligner/caller pair.
• UNRESTRICTED has both HG001 and HG002, but with caveats around precision. This set includes more total variants and two samples, but precision is less accurate.

Software addition:

• Sniffles v2.0.2 was added as a new caller

• Primarily adds dysgu v1.3.4 to both PCR-free and PacBio deletion benchmarks
• Secondarily added combinations in PCR-free that were not previously available (e.g. octopus is now paired with all active aligner combinations)

• Added the first haplotyping caller to our results with cyrius-1.1.1; note that this caller is designed to work on short-read datasets and the upstream tooling (both reference and aligner) can have significant impact on its performance
• Updated versions of pbmm2 (1.4.0 -> 1.7.0) and pbsv (2.6.2 -> 2.8.0); there are some changes in performance between the previous versions so they are retained in this release; they will be removed in subsequent releases

Two variant caller updates:

• Clair3 was update to v0.1-r9: Our previous version was v0.1-r5, and it was running in a conda environment after some back-and-forth with the developers. They now have a docker image that is much easier to use, so we have switched to that for both the Illumina and PacBio tests.
• PEPPER-Margin-DeepVariant was added a full caller on version r0.7: Previously, we were treating this process as a BAM modifier (basically for phasing) and ignoring any variant calling results. With this change, it now operates as a variant caller and the VCF is analyzed with the rest of the callers. We are using the developer-released docker image for our analysis.
• We have removed old versions of both tools to avoid any confusion around the analysis implementation

Two main results changes:

• Adds the dnascope-0.5-202010.04-PO variant caller: This is the same data as dnascope-0.5-202010.04 but with a PASS-only filter applied to the VCF file. The short-read DNAscope callers uses the FILTER field to annotate variants that are rejected by the model as likely false positives. This has significant impact on the results and is recommended as best practice by the developers. Thanks to @DonFreed for helping diagnose the issue!
• Updates minimap2 aligner from v2.22 to v2.23: Overall, this had minimal impact in our benchmark. v2.22 will be retired from the benchmark next release.

Metadata changes:

• Adds a references folder for tracking references that are used in the analysis
• Adds the hg38_asm5_alt reference including links to the reference and a script demonstrating how the ALT contigs were remapped
• Adds the hg38_GIAB_masked reference including links to the reference and a dummy ALT file used for the pipeline

Results changes:

• Added the SNAP-2.0.0 caller that was recently released, this was run with the -hc- option so GATK-based results are expected to not be as accurate