DeepFilter: A Deep Learning Based Variant Filter for VarDict  

作　　者：Hao Zhang Zekun Yin Yanjie Wei Bertil Schmidt Weiguo Liu 

机构地区：[1]School of Software,Shandong University,Jinan 250100,China [2]Shenzhen Research Institute of Shandong University,Shenzhen 518057,China [3]Shenzhen Institute of Advanced Technology,Chinese Academy of Sciences,Shenzhen 518055,China [4]Institute for Computer Science,Johannes Gutenberg University,Mainz 55128,Germany

出　　处：《Tsinghua Science and Technology》2023年第4期665-672,共8页清华大学学报（自然科学版（英文版）

基　　金：This work was partially supported by the National Natural Science Foundation of China(NSFC)(Nos.62102231 and 61972231);the Shenzhen Basic Research Fund(No.JCYJ20180507182818013);the Key Project of Joint Fund of Shandong Province(No.ZR2019LZH007);Shandong Provincial Natural Science Foundation(No.ZR2021QF089);the PPP project from CSC and DAAD;Engineering Research Center of Digital Media Technology,Ministry of Education,China.

摘　　要：With the development of sequencing technologies,somatic mutation analysis has become an important component in cancer research and treatment.VarDict is a commonly used somatic variant caller for this task.Although the heuristic-based VarDict algorithm exhibits high sensitivity and versatility,it may detect higher amounts of false positive variants than callers,limiting its clinical practicality.To address this problem,we propose DeepFilter,a deep-learning based filter for VarDict,which can filter out the false positive variants detected by VarDict effectively.Our approach trains two models for insertion-deletion mutations(InDels)and single nucleotide variants(SNVs),respectively.Experiments show that DeepFilter can filter at least 98.5%of false positive variants and retain 93.5%of true positive variants for InDels and SNVs in the commonly used tumor-normal paired mode.Source code and pre-trained models are available at https://github.com/LeiHaoa/DeepFilter.

关 键 词：variant filter deep learning somatic variant 

分 类 号：TP242[自动化与计算机技术—检测技术与自动化装置] TP18[自动化与计算机技术—控制科学与工程]