# Quality Filters

The Quality Filters allow one to filter variants by variant quality metrics. The filter can operate in a Simple or Advanced mode.

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## Modes

### Simple

Select a minimum degree of sequencing Quality (Low, Moderate, High).

### Advanced

#### **For SNVs and Indels:**

* Select a minimum degree of sequencing Quality (Low, Moderate, High),
* Define minimum Mapping Quality (0-60 - value can be exceeded using the text box),
* Specify minimum Depth (0-500 - value can be exceeded using the text box),
* Set minimum number of alternate reads in Alternate Read (0-500 - value can be exceeded using the text box). **Note:** available for cases run with pipeline version 5.26+.
* Set limits on Allele bias (0-100). **Note:** when applied to mtDNA variants, the Allele bias filter operates on heteroplasmy levels.

#### **For CNVs:**

* Set limits on CNV Length (50bp, 1kb, 10kb, 100kb, 1Mb, 100Mb, Max CNV length),
* Set minimum CNV Bin Count (1, 5, 10, 25, 50, 100, 500).

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## Default values

When [Filters](filters_presets_panel) are Reset to Default, The Quality Filters are set to:

* Quality: Moderate and High,
* Mapping Quality ≥45,
* Depth ≥ 10,
* Alternate Read - no filtering,
* Allele bias - no filtering,
* CNV Length - no filtering,
* CNV Bin Count - no filtering.

As of version 2.26:

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-95897e992ac60c817da4041b4d2bada32856e921%2Fquality_filters_1_filters_2_26.gif?alt=media)
