--- title: GermVar Tertiary - Are the variants from my input VCF filtered? description: "A guide to VCF filtering in GermVar Tertiary. Learn about region-based filtering, technical requirements (PASS, DP, VAF), and the specific \"split\" filtering strategy for WGS projects." --- [Skip to content](https://hubspot.seqone.com/test_seqone/germvar-tertiary-are-the-variants-from-my-input-vcf-filtered#main-content) English Show submenu for translations SeqOne Open main navigation Close main navigation - English Show submenu for translations - Contact us Contact us How can we help you? - There are no suggestions because the search field is empty. 1. [Test\_SeqOne](https://hubspot.seqone.com/test_seqone?hsLang=en) 2. [Technical Information](https://hubspot.seqone.com/test_seqone/technical-information?hsLang=en) 3. [Technical details](https://hubspot.seqone.com/test_seqone/technical-information?hsLang=en#technical-details) # GermVar Tertiary - Are the variants from my input VCF filtered? ## Understand the specific hard-coded filters applied to WGS, WES, and Panel tertiary analyses to remove artifacts and irrelevant calls. If you are using **GermVar Tertiary** to analyze your VCF files, you may have noticed a discrepancy between the number of variants in your input file and the number displayed in the SeqOne variant table. If you are looking for a specific variant but cannot find it, it may have been removed by our quality filters. This article details the specific filtering logic applied by GermVar Tertiary to help you understand what data is retained. #### 💡 Why do we filter input VCFs? We apply specific filters to your input VCF. This is done to avoid displaying an unmanageable list of variants and to help you eliminate artifacts, non-relevant calls, and common polymorphisms right from the start. The filtering logic depends on your project type (WGS, WES, or Panel). --- ### 1. WGS Projects (Genome) 🧬 For Whole Genome Sequencing (WGS) projects, we apply a "Split" strategy to balance sensitivity in coding regions with stricter filtering in non-coding regions. **🗺️  Region Filtering** We restrict the analysis to **RefSeq transcripts (NM in autosomal sequence only)** with a **±5000bp padding** at the start and end, plus Mitochondrial DNA. Anything outside these regions will be removed. **⚕️Clinical Filters** **We use a "split" logic:** variants within this region are divided into two lists and filtered differently: - **List 1: Coding Regions (CDS ±20bp):** - We keep **ALL** variants in these regions (subject to the technical filters below). - **List 2: Non-Coding Regions (The rest of the ±5000bp window):** We apply a frequency and pathogenicity filter. - **Excluded:** Variants that are **common** (GnomAD AF ≥ 5%) **AND** are **not** classified as Pathogenic or Likely Pathogenic in ClinVar. - *Result:* Rare variants and known pathogenic variants are kept; common benign polymorphisms are removed. **⚙️ Technical Filters** - **Filter Status:** We only keep variants with a `"PASS"` tag in the FILTER column. This status will be assigned by your secondary caller. - **Data Presence:** Variants must have **DP** (Depth) and **VAF** (Variant Allele Frequency, derived from AD/AO). - **Clean ALT:** We remove variants where ALT is `.`, `*`, or ``. - **Depth:** We remove variants with `DP=0`.   #### 💡 Note on technical filters: These values all come from your input VCF and have been assigned by your secondary caller. We apply some filters to make sure that all variants have the necessary information to be processed by SeqOne (Depth, VAF or metrics to compute it, clean ALT allele) and that they pass your caller's confidence filters.   --- ### 2. WES Projects (Exome) 🧬 For Whole Exome Sequencing (WES) projects, the filtering is focused on the captured exome regions. **🗺️  Region Filtering** - **RefSeq Exons ±20bp padding** - Mitochondrial DNA **⚕️Clinical Filters** - **No Frequency Filtering:** We **do not** filter based on GnomAD frequency or ClinVar status for WES. **⚙️ Technical Filters** - **Filter Status:** We only keep variants with a `"PASS"` tag. This status will be assigned by your secondary caller. - **Data Presence:** Variants must have **DP** and **VAF** (AD/AO). - **Clean ALT:** We remove variants where ALT is `.`, `*`, or ``. - **Depth:** We remove variants with `DP=0`.   --- ### 3. Panel Projects 🔬 For gene panel projects, the filtering is strictly defined by your specific design. **🗺️ Region Filtering** - **Manifest Only:** We only keep variants located within the regions defined in your manifest file. **⚕️Clinical Filters** - **No Frequency Filtering:** We **do not** filter based on GnomAD frequency or ClinVar status for Panels. **⚙️ Technical Filters** - **Filter Status:** We only keep variants with a `"PASS"` tag. This status will be assigned by your secondary caller. - **Data Presence:** Variants must have **DP** and **VAF** (AD/AO). - **Clean ALT:** We remove variants where ALT is `.`, `*`, or ``. - **Depth:** We remove variants with `DP=0`.   - [Releases](https://hubspot.seqone.com/test_seqone/releases?hsLang=en#main-content) - [Spring 2026](https://hubspot.seqone.com/test_seqone/releases?hsLang=en#spring-2026) - [Release Notes 2025](https://hubspot.seqone.com/test_seqone/releases?hsLang=en#release-notes-2025) - [What's new in Preview?](https://hubspot.seqone.com/test_seqone/releases?hsLang=en#whats-new-in-preview) - [Analysis & Interpretation](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#main-content) - [Variant table](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#variant-table) - [Workflow Management](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#workflow-management) - [Annotation and Scores](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#annotation-and-scores) - [Reporting](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#reporting) - [DiagAI](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#diagai) - [Coverage and Metrics](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#coverage-and-metrics) - [CNV](https://hubspot.seqone.com/test_seqone/analysis-interpretation?hsLang=en#cnv) - [Getting started](https://hubspot.seqone.com/test_seqone/getting-started?hsLang=en#main-content) - [General Platform Usage](https://hubspot.seqone.com/test_seqone/getting-started?hsLang=en#general-platform-usage) - [Intro to worksets](https://hubspot.seqone.com/test_seqone/getting-started?hsLang=en#intro-to-worksets) - [Video Tutorials](https://hubspot.seqone.com/test_seqone/getting-started?hsLang=en#video-tutorials) - [Files](https://hubspot.seqone.com/test_seqone/getting-started?hsLang=en#files) - [Intro to Platform Features](https://hubspot.seqone.com/test_seqone/getting-started?hsLang=en#intro-to-platform-features) - [Troubleshooting](https://hubspot.seqone.com/test_seqone/troubleshooting?hsLang=en#main-content) - [General](https://hubspot.seqone.com/test_seqone/troubleshooting?hsLang=en#general) - [Credentials](https://hubspot.seqone.com/test_seqone/troubleshooting?hsLang=en#credentials) - [Error and info messages](https://hubspot.seqone.com/test_seqone/troubleshooting?hsLang=en#error-and-info-messages) - [Information Security & Compliance](https://hubspot.seqone.com/test_seqone/information-security-compliance?hsLang=en#main-content) - [General](https://hubspot.seqone.com/test_seqone/information-security-compliance?hsLang=en#general) - [AI Systems Documentation](https://hubspot.seqone.com/test_seqone/ai-systems-documentation?hsLang=en#main-content) - [DiagAI Autofill](https://hubspot.seqone.com/test_seqone/ai-systems-documentation?hsLang=en#diagai-autofill) - [DiagAI HPO](https://hubspot.seqone.com/test_seqone/ai-systems-documentation?hsLang=en#diagai-hpo) - [Technical Information](https://hubspot.seqone.com/test_seqone/technical-information?hsLang=en#main-content) - [Workflows - Somatic](https://hubspot.seqone.com/test_seqone/technical-information?hsLang=en#workflows-somatic) - [Technical details](https://hubspot.seqone.com/test_seqone/technical-information?hsLang=en#technical-details) - [Databases](https://hubspot.seqone.com/test_seqone/technical-information?hsLang=en#databases) # SeqOne [mailto:email@email.com](mailto:email@email.com) Copyright © 2026, SeqOne