> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-variant-quality-filters.md). # 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](/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-filter-by-variant-category.md). ## 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](/connected-insights/configure/configuration/du-introduction/du-supported-pipelines.md) 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](/connected-insights/configure/configuration/du-introduction/du-supported-pipelines.md) 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](/connected-insights/resources-and-references/rar-acronyms-and-terms.md). --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-variant-quality-filters.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.