BACKGROUND Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now entering clinical practice. Consequently, variant analysis is increasingly important to facilitate a better understanding of disease entities and prognoses. Furthermore, variant calling allows to adapt and optimize specific treatments of individual patients, and thus is an integral part of personalized medicine.However, the analysis of NGS data typically requires a number of complex bioinformatics processing steps. A flexible and reliable software that combines the variant analysis process with a simple, user-friendly interface is therefore highly desirable, but still lacking. RESULTS With AMLVaran (AML Variant Analyzer), we present a web-based software, that covers the complete variant analysis workflow of targeted NGS samples. The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists. AMLVaran's interactive website presents comprehensive annotation data and includes curated information on relevant hotspot regions and driver mutations. A concise clinical report with rule-based diagnostic recommendations is generated.An AMLVaran configuration with eight variant calling tools and a complex scoring scheme, based on the somatic variant calling pipeline appreci8, was used to analyze three datasets from AML and MDS studies with 402 samples in total. Maximum sensitivity and positive predictive values were 1.0 and 0.96, respectively. The tool's usability was found to be satisfactory by medical professionals. CONCLUSION Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants. AMLVaran performs reliable NGS variant analyses and generates reports fulfilling the requirements of a clinical setting. Due to its generic design, the software can easily be adapted for use with different targeted panels for other tumor entities, or even for whole-exome data. AMLVaran has been deployed to a public web server and is distributed with Docker scripts for local use.

中文翻译：

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AMLVaran：一种软件方法，可在肿瘤护理环境中对目标NGS测序数据进行变异分析。

背景技术下一代测序（NGS）使得能够对遗传样品进行大规模且成本有效的测序，以检测遗传变异。在成功地用于研究型项目之后，NGS现在进入临床实践。因此，变异分析对于促进更好地了解疾病实体和预后变得越来越重要。此外，变体调用允许适应和优化个别患者的具体治疗方法，因此是个性化医学的组成部分。但是，NGS数据的分析通常需要许多复杂的生物信息学处理步骤。因此，非常需要一种灵活而可靠的软件，该软件将变体分析过程与简单，用户友好的界面相结合，但仍然缺乏。使用AMLVaran（AML变量分析器）的结果，我们提供了一个基于Web的软件，该软件涵盖了目标NGS样品的完整变体分析工作流程。该软件提供了一个通用管道，允许自由选择变体调用工具和灵活的语言（SSDL）来过滤变体列表。AMLVaran的交互式网站提供了全面的注释数据，并包括有关相关热点区域和驾驶员突变的精选信息。生成具有基于规则的诊断建议的简明临床报告。基于体细胞变异调用管道appreci8的AMLVaran配置，八种变异调用工具和复杂的评分方案用于分析AML和MDS研究的三个数据集，包含402个样本总共。最大灵敏度和阳性预测值分别为1.0和0.96。工具' 医学专业人员发现其可用性令人满意。结论覆盖率分析，可再现的变体过滤和软件可用性对于变体的临床评估很重要。AMLVaran执行可靠的NGS变异分析并生成满足临床环境要求的报告。由于其通用设计，该软件可以轻松地与其他肿瘤实体甚至整个外显子数据的不同目标面板一起使用。AMLVaran已部署到公共Web服务器，并与Docker脚本一起分发以供本地使用。AMLVaran执行可靠的NGS变异分析并生成满足临床环境要求的报告。由于其通用设计，该软件可以轻松地与其他肿瘤实体甚至整个外显子数据的不同目标面板一起使用。AMLVaran已部署到公共Web服务器，并与Docker脚本一起分发以供本地使用。AMLVaran执行可靠的NGS变异分析并生成满足临床环境要求的报告。由于其通用设计，该软件可以轻松地与其他肿瘤实体甚至整个外显子数据的不同目标面板一起使用。AMLVaran已部署到公共Web服务器，并与Docker脚本一起分发以供本地使用。