Polymorphism Filters

The Polymorphism Filters enable filtering variants by alternative allele frequencies and genotype counts in public and internal databases. The filters can operate in a Simple or Advanced mode.

Simple mode

Switch on or off Display Polymorphism option:

• When switched on, no restrictions are being applied.

• When switched off, variants with allele frequency >0.05 in public databases or >0.25 in the EmedgeneDB are filtered out.

Advanced mode

Filter variant list by limiting the maximum Allele Frequency, Hom/Hemi and Het counts in one of the public database options (GnomAD, ExAC, 1000 Genomes, or GME) or, by default, in all (All Databases). The default values for Hom/Hemi and Het can be exceeded using the text box.

In addition, limit results by the maximum Allele Frequency in internal databases:

• Emedgene Database - a static sample set of 806 healthy individuals. Aimed at getting rid of the artifacts generated by our FASTQ processing pipeline

• Organization Databases, e.g., NoiseDB - a blacklist of variants (implemented by request).

Default values

When Filters are Reset to Default, The Polymorphism Filters are set to the Display Polymorphism option of the Simple mode, i.e., no filtering.