Germline WGS
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This recipe is for processing whole genome sequencing data for germline workflows.
For most scenarios, simply creating the union of the command line options from the single caller scenarios will work.
Configure the INPUT options
Configure the OUTPUT options
Configure MAP/ALIGN depending on if realignment is desired or not
Configure the VARIANT CALLERs based on the application
Configure any additional options
Build up the necessary options for each component separately, so that they can be re-used in the final command line.
We highly recommend using a pangenome reference for human samples (excluding RNA). For more details, refer to .
The following are partial templates that can be used as starting points. Adjust them accordingly for your specific use case.
enable-hla
Enable HLA typer (this setting by default will only genotype class 1 genes)
hla-enable-class-2
Extend genotyping to HLA class 2 genes
Optional settings per component are listed below. Full option list at .
Note that we do not recommend changing the default QUAL thresholds of 3 for DRAGEN-ML and 10 for DRAGEN without ML. These values differ from each other because DRAGEN-ML improves the calibration of QUAL scores, leading to a change in the scoring range (see ).