Compatible callers for non human references in the DRAGEN Germline App

When analyzing non-human references with DRAGEN Germline v4.4, only a subset of variant callers are supported.

The following features are compatible with non-human analysis:

• SNV

• CNV

  • requires --cnv-bypass-contig-check=true as additional command line argument

  • Allele-specific CNV Calling option is not supported

• SV

The following features are incompatible with non-human analysis:

• Tandem Repeats Caller (STR, VNTR)

• Targeted Callers (cyp2d6, cyp21a2, gba, smn, hba, rh, lpa)

• HLA Typing

• Star Allele Caller

• Variant annotation

• QC Detect Contamination

Refer to the DRAGEN Reference Support article for a full list of supported features.

For any feedback or questions regarding this article (Illumina Knowledge Article #9848), contact Illumina Technical Support [email protected].