DeepFilter:一种基于深度学习的VarDict变量滤波器

IF 5.2 1区 计算机科学 Q1 COMPUTER SCIENCE, INFORMATION SYSTEMS Tsinghua Science and Technology Pub Date : 2023-01-01 DOI:10.26599/TST.2022.9010032
Hao Zhang;Zekun Yin;Yanjie Wei;Bertil Schmidt;Weiguo Liu
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引用次数: 0

摘要

随着测序技术的发展,体细胞突变分析已成为癌症研究和治疗的重要组成部分。VarDict是此任务中常用的体细胞变体调用程序。尽管基于启发式的VarDict算法表现出高灵敏度和多功能性,但它可能比呼叫者检测到更多的假阳性变体,限制了其临床实用性。为了解决这个问题,我们提出了一种基于深度学习的VarDict过滤器DeepFilter,它可以有效地过滤掉VarDict检测到的假阳性变体。我们的方法分别训练插入缺失突变(InDels)和单核苷酸变异(SNV)的两个模型。实验表明,在常用的肿瘤-正常配对模式下,DeepFilter可以过滤至少98.5%的假阳性变体,并保留93.5%的InDels和SNVs的真阳性变体。源代码和预训练模型可在https://github.com/LeiHaoa/DeepFilter.
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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DeepFilter: A Deep Learning Based Variant Filter for VarDict
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CiteScore
12.10
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