# 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.


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/haplotype-variant-quality-metrics.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.