# 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.`