> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/haplotype-variant-quality-metrics.md).

# Haplotype variant quality metrics

The following metrics are calculated for haplotype variants.

## Zygosity

* Indicates whether the haplotype is present on one chromosome or both, based on the genotype reported in the VCF.

## VCF Filter

* Displays the value of the `FILTER` field in the VCF.
* Reflects whether the haplotype variant passed DRAGEN quality thresholds or failed one or more checks (e.g., depth, allele balance, phasing constraints).
* The platform shows the `FILTER` flag exactly as provided by the caller.
* Requires DRAGEN 4.3+.

## Min. Genotype Quality

* Shows the genotype confidence score assigned by the caller.
* Higher `GQ` values indicate greater confidence in the phased genotype behind the haplotype.

### Copy Number (v100.41.0+)

* Displayed when available for haplotype variants generated by the DRAGEN MRJD caller (4.5).
* Shows the copy number assigned to the haplotype variant within its region group.


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