Known Limitations

Functionality

• This software solution will only work with the 5-base Library Prep kit

  • DRAGEN Methylation can be run on 5-base data, but it will produce lower alignment and no variant calls

• Somatic Tumor/Normal analysis is not supported in Enrichment workflows

• CNV analysis is not supported in Enrichment workflows

• SV results are turned on to improve CNV calling accuracy, but these results are not verified or supported

Performance

• 5-base alignment may underperform on genomes with significant non-CpG methylation levels

• M-bias calculations are inaccurate for R2 for cfDNA samples when using default settings

  • Recommendation is to add --mbias-report-include-overlaps=true for this use case

• Integrated downsampling is not functional for DRAGEN Enrichment

  • If downsampling is required, run with the fractional downsampler in the DRAGEN FASTQ Toolkit

Variant Calling

• Any additional variant callers are not supported, and any data generated by them has not been validated

• Variant calling is only currently supported for human reference genomes

  • If required, non-human reference genomes must be uploaded in a v11 file format. These will not produce variant calls that the Illumina team supports. The following error will be displayed in ICA, but the run will complete: WARNING: --methylation-conversion=illumina is only supported on human references.