DRAGEN Array Genotyping and QC

Custom Configuration Options

When using DRAGEN Array – Genotyping and QC cloud analysis type, you have the following configuration options available via the "Add Custom Configuration" option in Configuration Settings:

• Output File Selection: Flexibility to turn off/on specific output files

  • VCF output can be toggled on or off

  • Final Report output can be toggled on or off

  • Locus Summary output can be toggled on or off

• GenCall Score Cutoff: Adjustable threshold for genotype calling quality

  • Override default GenCall score cutoff

• Use Infinium I probe no-calls: Constrain possible genotypes using Infinium I probe no-call information.

• QC Report Output Format: Excel (xlsx) - default or CSV format. For more information, see DRAGEN Array QC Report.

Recommendations

• For non-human species: It is recommended to turn off VCF output, as VCF generation requires genome mapping which is only provided for human genomes (GRCh37 and GRCh38).

• For large sample numbers (~400+ samples): It is recommended to turn off Final Report output, as Final Report files can reach 50+ GB and become difficult to download.

Applicable Arrays

For specific product compatibility, see the Product & Analysis Compatibility table.