Geneyx Analysis: Our Most Significant Updates to Date
Geneyx Analysis 6.0: DRAGEN Advanced Callers
DRAGEN version selection: Users now have the option to select the version of DRAGEN that is being utilized for the secondary pipeline. The baseline DRAGEN version will remain v4.0.5. This option will allow users to conform to their existing workflows while also enabling the exploration of updated DRAGEN features. The optional DRAGEN version (4.2.4) enables several additional features, discussed below, including advanced callers and low pass whole genome options. For upgrading to the newest Dragen caller.
*Please be aware that overtime DRAGEN v4.0.5 will be deprecated.
DRAGEN v4.2.4: The comprehensive updates included in DRAGEN v4.2.4 can be found here. At a high level, this update includes improvements to small variant calling at high depths for WGS (>100X), High sensitivity mode results in increased sensitivity for reads with low MAPQ and low allele frequency (mosaic variants), Joint CNV/SV signal improves CNV detection for events ranging from 1-10kbp.
Advanced DRAGEN Callers: When running whole genome workflows from the secondary pipeline, there are new sequence-graph realignment settings that run on the backend to improve calling for genes that have high identity paralogs. This includes genes such as: GBA, SMN1, HBA, LPA, RH, CYP2D6, CYP21A2, CYP2B6. For analyses that have whole genome workflows with at least 30X coverage, output metrics for these genes will be present in the Advanced Analysis link in the “Info” section of the analysis. All outputs are taken from Illumina and each output will reference the associated hyperlink.
DRAGEN Low pass whole genome sequencing: Low-pass whole genome sequencing (low-pass WGS) is a genomic sequencing approach where the entire genome is sequenced at a relatively low depth, typically less than 5x coverage. Low pass whole genome sequencing is now supported in the secondary pipeline of Geneyx. To implement, the sequencing target will need to set to Whole Genome Low Pass.
