Pipeline versions

The Pipeline version card, located in the Workbench & Pipeline section of Organization Settings, allows you to set the applied versions for the sample pipeline, case pipeline, DRAGEN, and human reference. You can also configure whether to include reference homozygous genotype calls in cases.

Pipeline versions card

Sample

Set the organization sample pipeline configurations. These configurations are only applicable for cases starting from FASTQ files.

• Human Ref- Set the used human reference genome build to apply in the pipeline, used for alignment and calling. possible options: GRCh37 and GRCh38.

• Secondary Analysis Pipeline- Set the used secondary analysis pipeline for your organization. This pipeline shall be applicable for all FASTQ samples that are part of the case.

• DRAGEN Version- Set the used DRAGEN version utilized in the Secondary analysis pipeline.

Variant caller mapping

Select the variant callers enabled for your secondary analysis pipeline.

Each caller is annotated with its sequencing compatibility (WGS, WES), methodology (e.g., CNV read-depth, small variant, SV split-end), and compatibility requirements across sample, DRAGEN, and case pipeline versions. By default, SNV and CNV callers are always enabled. Additional callers, such as SV, SMN, and STR can now be selectively activated to match evolving analysis needs. Changes made through this interface will apply to newly processed cases after changing selected callers.

Enabling variant caller that is not compatible with the selected pipelines is not supported.

Some variant callers may require an assigned PON file to apply properly for WES sequencing type.

Sample pipeline arguments

View your Sample pipeline arguments for mapping and calling. In order to modify these arguments, you will need to contact technical support.

If the arguments are not set, they will be displayed as ‘N/A’.

Case

Set the organization case pipeline configuration. This configuration is applicable for all cases in your organization.

Changing the case pipeline will affect the used annotation sources and version for your cases and may impact AI shortlist outcome for your case.