Release 2022-06-10

Tool changes:

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

Release 2022-05-19

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

Release 2022-04-29

• 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

Release 2022-04-08

• 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

Release 2022-03-18

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

Release 2022-02-25

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.

Release 2022-02-18

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

Release 2022-02-11

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.

Release 2022-02-09

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!

Release 2022-02-08

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