Quality Filters

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


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).


Default values

When Filters 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:

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