Variant Quality Filters

This page summarizes filters related to variant quality. Filter availability can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same condition group, only filters relevant for all variant categories are available. For more information, refer to Filter by Variant Category.

Filters

Filters data by the value provided for the variant in the FILTER column of the VCF file. Refer to the variant caller documentation in Supported Pipelines to confirm possible values and recommended thresholds.

Quality

Filters data by the value provided for the variant in the QUAL column of the VCF file. Refer to the variant caller documentation in Supported Pipelines to confirm possible values and recommended thresholds.

Sample Metrics

Filters data by read metrics, for example, VAF, allele depth, paired and read counts, split read count, and others.

Low Complexity Region

Excludes small variants in low complexity regions (LCRs).

For more information, refer to Acronyms and Terms.