Polymorphism filters

The Polymorphism Filters enable filtering variants by alternative allele frequencies and genotype counts in public and internal databases.

The Polymorphism 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.

Simple mode

Use the Display Polymorphism toggle to enable or disable filtering:

• On: No filtering is applied

• Off: Variants with maximum allele frequency >0.05 in public databases are excluded

Advanced mode

1. Select data source

Select the source for population statistics:

• A specific database

• All databases

By default, "All databases" is selected.

Available databases:

• SNV, STR:

  • gnomAD

  • ExAC

  • 1000 genomes

  • GME

• SV, CNV:

  • gnomAD SV

  • DGV Gold

  • Decipher Healthy Population

2. Set filters

Apply the filters to the selected source.

Maximum allele frequency

Maximum allele frequency in the selected source.

• Range: 0–0.05 using the slider

• Custom value: Enter a number in the input field (value can exceed 0.05 but cannot be greater than 1)

Maximum Hom/Hemi count

Hom/Hemi count—the number of individuals who are homozygous/hemizygous for the variant in the selected source.

• Range: 0–100 using the slider

• Custom value: Enter a number in the input field (value can exceed 100)

• Max: Disables filtering for this parameter

Maximum allele count

Maximum allele count in the selected source.

• Range: 0–500 using the slider

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

• Max: Disables filtering for this parameter

Maximum allele frequency in Emedgene internal database

Maximum allele frequency in a sample of 806 healthy individuals, designed to eliminate artifacts introduced by the FASTQ processing pipeline.

• Range: 0–0.05.

• Custom value: Enter a number in the input field (value can exceed 0.05 but cannot be greater than 1)

Maximum allele frequency in organizational databases

Maximum allele frequency within the internal databases of an organization (Historic or Noise).

• Range: 0–0.05

• Custom value: Enter a number in the input field (value can exceed 0.05 but cannot be greater than 1)

Default values

When Filters are Reset to Default, The Polymorphism filters are not applied.