# Quality filters

Use Quality filters to refine variant reviews by setting **quality thresholds** and filtering based on **calling methodology**. This prioritizes variants that meet specific confidence metrics for interpretation.

The Quality filters can operate in a [Simple ](#simple-mode)or [Advanced ](#advanced-mode)mode.

{% hint style="warning" %}
**Simple and advanced filtering modes operate independently.**

Even with similar settings, results may differ due to variations in filtering logic and options available.
{% endhint %}

{% hint style="success" %}
**Tips:**

* Start with **Simple Mode** for quick triaging, then refine using **Advanced Mode**
* Always cross-check low-quality calls in **IGV visualization** before discarding
  {% endhint %}

## Simple mode

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-9c47908d8826af23d75b9a95e040bfbc0c90832e%2Fquality%20simple.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Quickly filter variants by minimum overall sequencing quality:

* **Low**: No quality filtering applied
* **Moderate**: Includes moderate and high quality variants with read depth ≥10
* **High**: Includes only high quality variants with read depth ≥10
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## Advanced mode

Provides fine-grained control over multiple quality metrics depending on the variant type.

### Quality

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-54c9d7f1637b16e04b0a6af3f8a6aaef74eda2bd%2Fquality%20filter%20advanced%20quality%201.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Aggregated quality specific to variant type and caller. Determines overall confidence score thresholds for all variant types.

* **Low**
* **Moderate**
* **High**
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### VCF FILTER

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-d9d28ad512098b6b5b10e0ff81e601b9171ef6f2%2Fquality%20filter%20advanced%20VCF.gif?alt=media" alt=""><figcaption></figcaption></figure>
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FILTER column value in VCF.

* **Pass**: Variants with PASS value
* **Other values**: Variants with any value except PASS
  {% endcolumn %}
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### Calling methodology

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-a2f05af7ca6a14b8bfdbfab82e2b8ef7698c8403%2Fquality%20filter%20advanced%20calling%20method.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Calling methodology filter allows filtering by [variant caller](https://help.emg.illumina.com/emedgene-analyze-manual/supported-vcfs-variant-callers) type.

* **Small Variant**
* **CNV Read-Depth**
* **Forced Genotyping**
* **Star Allele**
* **STR Repeat Expansion**
* **SV Split-End**
* **Targeted**
* **MRJD**
* **Array**
* **Unknown**

{% hint style="success" %}
**Note:** This is especially useful for filtering CNVs from different callers (e.g., DRAGEN Read-Depth vs. SV Caller) to apply separate noise databases or QC settings.
{% endhint %}
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### Quality metrics by variant type: **SNV, indel, MNV (v100.39.0+), and STR**

#### Mapping quality (MQ)

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-28bfb8563a9bc007efd6a55b96969235f55b550d%2Fquality%20filter%20advanced%20MQ.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Minimum mapping quality.

* **Range**: 0–60 using the slider
* **Custom value**: Enter a number in the input field (value can exceed 60)
  {% endcolumn %}
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#### Depth (DP)

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-16faf8732c514a805554fa6095faf622ee74daf1%2Fquality%20filter%20advanced%20DP.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Minimum read depth.

* **Range**: 0–500 using the slider
* **Custom value**: Enter a number in the input field (value can exceed 500)
  {% endcolumn %}
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#### Alternate read count

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-be158a4ea6bbb64058c16ca2c5b1f8251badd119%2Fquality%20filter%20advanced%20alt%20read.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Minimum number of reads supporting the alternate allele.

* **Range**: 0–500 using the slider
* **Custom value**: Enter a number in the input field (value can exceed 500)
  {% endcolumn %}
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#### Allele bias

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-0467e0cf851ee6f48497e957411306f43afd8002%2Fquality%20filter%20advanced%20allele%20bias.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Minimum and maximum allowable allele bias. For mtDNA, this represents heteroplasmy level.

* **Range:** 0–100 using two sliders (minimum and maximum)

{% hint style="warning" %}
When analyzing a VCF file that includes **CNV variants with** [**AD**](#user-content-fn-1)[^1] **values**, be aware that these variants—along with SNVs—may also be impacted by the allele bias filter.
{% endhint %}
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### Quality metrics by variant type: **SV, CNV, and LOH/ROH**

#### Length

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-b7c09fad0f4f304fd56707055e288113f081b305%2Fquality%20filter%20advanced%20SV%20length.gif?alt=media" alt=""><figcaption></figcaption></figure>
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{% column width="58.33333333333333%" %}
Sets the minimum and maximum variant size using two sliders.

* **Supported values**: 50 bp, 1 kbp, 10 kbp, 100 kbp, 1 Mbp, 10 Mbp, Max.
  * **Max:** When selected as the upper threshold, all CNVs 50 bp and larger are shown.
    {% endcolumn %}
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#### Bin Count

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<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-07d39b6ac41d7a2d27bd574cd4545922e313d4d8%2Fquality%20filter%20advanced%20bin%20count.gif?alt=media" alt=""><figcaption></figcaption></figure>
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Minimum bin count.

* **Range**: 0–500 using the slider
* **Custom value**: Enter a number in the input field (value can exceed 500)
  {% endcolumn %}
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{% hint style="warning" %}
When analyzing a VCF file that includes CNV variants with AD[^1] values, be aware that these variants—along with SNVs—may also be impacted by the **Allele bias** **filter**.
{% endhint %}

## Default values

When filters are reset to default, the Quality filters are set to:

<table><thead><tr><th width="238">Filter</th><th width="238">Setting</th></tr></thead><tbody><tr><td><strong>Quality</strong></td><td><strong>Moderate, High</strong></td></tr><tr><td><strong>Mapping Quality</strong></td><td><strong>≥45</strong></td></tr><tr><td><strong>Depth</strong></td><td><strong>≥10</strong></td></tr><tr><td>Other Quality filters</td><td>No restriction</td></tr></tbody></table>

[^1]: Allele Depth — total read depth for each allele according to the Variant Call Format specification.