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.

VCF 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.

For TruSight Oncology 500, filtering by VCF Filters = PASS also returns variants with KeepFusion = TRUE in the fusion output file.

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 sample-level metrics for the tumor sample and normal sample (in the case of tumor + normal analysis):

• Allele Depth

• Total Depth

• Split Reads

• Paired Reads

• Supporting Reads

• VAF

• Somatic Quality

Low Complexity Region

Excludes small variants in low complexity regions (LCRs).

For more information, refer to Acronyms and Terms.