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Current status for GDx-bioinf systems and reference datasets

Internal (OUS in-house) frequency database information

The following information provides details on the most recent updates to our in-house variant frequency databases.

General sample inclusion criteria: This encompasses parental and single non-redundant samples, with the exclusion of test and control samples.

Additional criteria for CNV/SV databases: The analysis results are confined to deletions (DEL) and duplications (DUP and DUP:TANDEM), and the calls produced using Dragen.

Database Database content Individuals, count Last updated Oldest project Newest project
OUSWGS SNV/indel allele frequency from wgs 5871 2023-04-29 first wgs wgs249
OUSWES SNV/indel allele frequency from exomes 7003 2022-02-02 first exome excap230
OUS Manta DB SV allele frequency from wgs, Manta caller 4690 2023-02-27 wgs140 wgs252
OUS Canvas DB CNV allele frequency from wgs, Canvas caller 7710 2023-02-27 wgs28 wgs252

Core production systems

The table below lists the latest release for important source code repositories. Follow links for previous releases.

System Repository Version
Automation TSD import and LIMS integration (tsd-import) Latest release
Automation Maestro [none]
Automation Steps [none]
Variant calling Variant calling pipeline (vcpipe) Latest release
Variant calling Noninvasive prenatal testing (NIPT) [none]
Annotation anno Latest release
Annotation anno-targets Latest release
Annotation Post-processing of structural variants (sv-pack) [TODO: create release page] v1.3.0
Interpretation ELLA Latest release
Interpretation Gene panel builder (GPB) Latest release
Interpretation Gene panel store Latest release