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 or Advanced mode.

Simple and advanced filtering modes operate independently.

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

Tips:

• Start with Simple Mode for quick triaging, then refine using Advanced Mode

• Always cross-check low-quality calls in IGV visualization before discarding

Simple mode

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

Advanced mode

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

Quality

Aggregated quality specific to variant type and caller. Determines overall confidence score thresholds for all variant types.

• Low

• Moderate

• High

VCF FILTER

FILTER column value in VCF.

• Pass: Variants with PASS value

• Other values: Variants with any value except PASS

Calling methodology

Calling methodology filter allows filtering by variant caller type.

• Small Variant

• CNV Read-Depth

• Forced Genotyping

• Star Allele

• STR Repeat Expansion

• SV Split-End

• Targeted

• MRJD

• Array

• Unknown

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.

Quality metrics by variant type: SNV, indel, MNV (v100.39.0+), and STR

Mapping quality (MQ)

Minimum mapping quality.

• Range: 0–60 using the slider

• Custom value: Enter a number in the input field (value can exceed 60)

Depth (DP)

Minimum read depth.

• Range: 0–500 using the slider

• Custom value: Enter a number in the input field (value can exceed 500)

Alternate read count

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)

Allele bias

Minimum and maximum allowable allele bias. For mtDNA, this represents heteroplasmy level.

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

When analyzing a VCF file that includes CNV variants with AD values, be aware that these variants—along with SNVs—may also be impacted by the allele bias filter.

Quality metrics by variant type: SV, CNV, and LOH/ROH

Length

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.

Bin Count

Minimum bin count.

• Range: 0–500 using the slider

• Custom value: Enter a number in the input field (value can exceed 500)

When analyzing a VCF file that includes CNV variants with AD values, be aware that these variants—along with SNVs—may also be impacted by the Allele bias filter.

Default values

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

Filter	Setting
Quality	Moderate, High
Mapping Quality	≥45
Depth	≥10
Other Quality filters	No restriction