---
title: FAQ & Troubleshooting | VarSome Help Center
description: "Answers for frequently asked questions from users and clients.\nProvide solution to known issues"
---
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1. [VarSome Help Center](https://docs.varsome.com/en)
2. [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting)
# FAQ & Troubleshooting
Answers for frequently asked questions from users and clients. Provide solution to known issues
- [CNV Quality Control: tools and guidelines](https://docs.varsome.com/en/cnv-quality-control)
- [VCF attributes explained](https://docs.varsome.com/en/vcf-attributes-explained)
- [How can I submit to ClinVar?](https://docs.varsome.com/en/how-can-i-submit-to-clinvar)
- [How can I inspect my analysis results on more than one monitors?](https://docs.varsome.com/en/how-can-i-inspect-my-analysis-results-on-more-than-one-monitors)
- [Mitochondrial variant calling](https://docs.varsome.com/en/mitochondrial-variant-calling)
- [How can I use a gene list analysis for CNV calling?](https://docs.varsome.com/en/how-can-i-use-a-gene-list-analysis-for-cnv-calling)
- [Common error messages when launching CNV analyses](https://docs.varsome.com/en/common-error-messages-when-launching-cnv-analyses)
- [Best practices for variant calling on VarSome Clinical](https://docs.varsome.com/en/best-practices-for-variant-calling-on-varsome-clinical)
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## Troubleshooting
- [Why is it important to process UMIs properly?](https://docs.varsome.com/en/why-is-it-important-to-process-umis-properly)
- [Why can't I see the variant table or log into VarSome Clinical?](https://docs.varsome.com/en/clear-cookies-and-cache-from-your-browser)
- [Why is the variant annotation different on VarSome and VarSome Clinical?](https://docs.varsome.com/en/why-is-the-variant-annotation-different-on-varsome-and-varsome-clinical)
- [Assay missing in the list](https://docs.varsome.com/en/assay-missing-in-the-list)
## General
- [How to identify the order of sample IDs in a multi-sample VCF file](https://docs.varsome.com/en/how-to-identify-the-order-of-sample-ids-in-a-multi-sample-vcf-file)
- [Pseudogenes](https://docs.varsome.com/en/pseudogenes)
- [Mitochondrial genome versions](https://docs.varsome.com/en/mito-genome-versions)
- [How can I link a publication to a variant?](https://docs.varsome.com/en/contributing-to-varsome)
- [Which assays with UMIs are supported by VarSome?](https://docs.varsome.com/en/supported-panels-with-umis)
- [What are the requirements for the trial period of VarSome Clinical?](https://docs.varsome.com/en/requirements-trial-of-varsome-clinical)
- [Variant Sharing Program](https://docs.varsome.com/en/variant-sharing-among-institutions)
- [Phasing](https://docs.varsome.com/en/phasing)
- [How to recalculate variants in phase that are called separately?](https://docs.varsome.com/en/how-to-recalculate-close-by-variants-in-phase)
- [Initiating VarSome Clinical Workflows with FASTQ vs. VCF Files](https://docs.varsome.com/en/initiating-varsome-clinical-workflows-with-fastq-vs-vcf-files)
- [Understanding VarSome Query Limits](https://docs.varsome.com/en/understanding-varsome-query-limits)
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## Filters
- [How can I filter my results by Frequency or Pathogenicity ?](https://docs.varsome.com/en/how-can-i-filter-my-results-by-frequency-or-pathogenicity)
- [How can I filter out artefacts from my samples?](https://docs.varsome.com/en/filter-out-artefacts)
## User Interface
- [Why are my column order preferences on VarSome Clinical not saved after I log out?](https://docs.varsome.com/en/why-are-my-column-order-preferences-on-varsome-clinical-not-saved-after-i-log-out)
- [Sequencing assay selection](https://docs.varsome.com/en/sequencing-kit-selection)
- [Investigating exon coverage](https://docs.varsome.com/en/investigating-exon-coverage)
- [Why do the clinical cards not change when I select one variant?](https://docs.varsome.com/en/clinical-cards-faq)
- [How can I launch an analysis of several independent samples?](https://docs.varsome.com/en/how-can-i-launch-an-analysis-of-several-independent-samples)
- [Adding an assay to VarSome Clinical](https://docs.varsome.com/en/adding-an-assay-to-varsome-clinical)
- [How can I quickly check the coverage for a specific exon of a given transcript or gene?](https://docs.varsome.com/en/how-can-i-quickly-check-the-coverage-for-a-specific-exon-of-a-given-transcript-or-gene)
- [Downloading variant annotation data](https://docs.varsome.com/en/downloading-variant-annotation-data)
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## Pipelines
- [Alignment and Calling](https://docs.varsome.com/en/alignment-and-calling)
- [Which reference genome is being used to align the reads?](https://docs.varsome.com/en/reference-genomes)
- [Targeted/Untargeted Calling on VarSome Clinical](https://docs.varsome.com/en/targeted-calling-on-varsome-clinical)
- [How can I validate my laboratory pipeline and bioinformatics results?](https://docs.varsome.com/en/how-to-validate-my-laboratory-pipeline)
- [Variant calling and quality filters](https://docs.varsome.com/en/variant-calling-and-quality-filters)
- [How is frequency calculated for CNV calls?](https://docs.varsome.com/en/how-is-frequency-calculated-for-cnv-calls)
- [Can I reuse a standard set of control samples to call CNVs?](https://docs.varsome.com/en/can-i-reuse-a-standard-set-of-control-samples-to-call)
- [Variant calling local reassembly](https://docs.varsome.com/en/variant-calling-local-reassembly)
- [Is there a minimum length of CNVs that can be detected by the CNV calling pipeline?](https://docs.varsome.com/en/what-is-the-minimum-length-of-cnvs-that-can-be-detected-by-the-cnv-calling-pipeline)
- [Splicing variants](https://docs.varsome.com/en/splicing-variants)
- [Joint calling](https://docs.varsome.com/en/joint-calling)
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## Features
- [VarSome Lighthouse (AI summary)](https://docs.varsome.com/en/varsome-lighthouse-ai-summary)
- [What is VarSome Picks?](https://docs.varsome.com/en/varsome-picks)
- [What is VarSome Clinical PGx?](https://docs.varsome.com/en/what-is-varsome-clinical-pgx)
- [Tumor Mutational Burden Estimation with VarSome Clinical](https://docs.varsome.com/en/tmb)
- [Microsatellite Instability (MSI) analysis on VarSome Clinical](https://docs.varsome.com/en/msi)
- [3D Protein Viewer](https://docs.varsome.com/en/protein-viewer)
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- [Registration & Billing](https://docs.varsome.com/en/registration-billing#main-content)
- [User account management](https://docs.varsome.com/en/registration-billing#user-account-management)
- [Storage management](https://docs.varsome.com/en/registration-billing#storage-management)
- [Pricing and Billing](https://docs.varsome.com/en/registration-billing#pricing-and-billing)
- [VarSome Clinical Tokens](https://docs.varsome.com/en/registration-billing#varsome-clinical-tokens)
- [Management of Samples and Analyses](https://docs.varsome.com/en/management-of-samples-and-analyses#main-content)
- [Uploading files](https://docs.varsome.com/en/management-of-samples-and-analyses#uploading-files)
- [Managing Samples](https://docs.varsome.com/en/management-of-samples-and-analyses#managing-samples)
- [Managing Workflows](https://docs.varsome.com/en/management-of-samples-and-analyses#managing-workflows)
- [Launching analyses](https://docs.varsome.com/en/management-of-samples-and-analyses#launching-analyses)
- [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results#main-content)
- [Analyses](https://docs.varsome.com/en/analysis-of-the-results#analyses)
- [Results](https://docs.varsome.com/en/analysis-of-the-results#results)
- [Filters](https://docs.varsome.com/en/analysis-of-the-results#filters)
- [Reporting](https://docs.varsome.com/en/analysis-of-the-results#reporting)
- [Quality Control](https://docs.varsome.com/en/analysis-of-the-results#quality-control)
- [Legal & compliance](https://docs.varsome.com/en/legal-compliance)
- [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting#main-content)
- [Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting#troubleshooting)
- [General](https://docs.varsome.com/en/faq-troubleshooting#general)
- [Filters](https://docs.varsome.com/en/faq-troubleshooting#filters)
- [User Interface](https://docs.varsome.com/en/faq-troubleshooting#user-interface)
- [Pipelines](https://docs.varsome.com/en/faq-troubleshooting#pipelines)
- [Features](https://docs.varsome.com/en/faq-troubleshooting#features)
- [Scientific articles](https://docs.varsome.com/en/scientific-articles)
- [VarSome API](https://docs.varsome.com/en/varsome-api)
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[Query Examples](https://varsome.com/about/resources/examples/)
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