VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data.
VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data.
复制标题
VCF.Filter：测序数据中疾病连接遗传变异的互动优先级。
DOI：
10.1093/nar/gkx425
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发表时间：
2017-07-03
影响因子：
14.9
通讯作者：
Bock C
中科院分区：
文献类型：
--
作者：
Müller H;Jimenez-Heredia R;Krolo A;Hirschmugl T;Dmytrus J;Boztug K;Bock C
下一代测序被广泛用于将遗传变异与疾病联系起来，它极大地加快了罕见遗传疾病的诊断和表征。在最初的生物信息学数据处理之后，基因组、外显子组和面板测序数据的交互分析通常从VCF格式的遗传变异列表开始。医学遗传学家对这些列表进行过滤和注释，以确定可能与所调查疾病相关的变异，或选择在临床诊断环境中报告的变异。我们开发了VCF。Filter，方便搜索与疾病相关的变体，为交互式变体过滤和注释提供了一个具有用户友好界面的独立Java程序。VCF。Filter允许用户通过图形界面定义广泛的过滤标准。常见的工作流（如三人组分析和基于队列的过滤）是预先配置的，更复杂的分析可以使用VCF执行。Filter对自定义注释和过滤标准的支持。所有的过滤都记录在结果文件中，从而提供交互式变量优先级的可跟踪性。VCF。Filter是一个开源工具，可以在http://vcffilter.rarediseases.at上免费公开获取。
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.
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影响因子：
12.3
作者：
McLaren W;Gil L;Hunt SE;Riat HS;Ritchie GR;Thormann A;Flicek P;Cunningham F
通讯作者：
Cunningham F
影响因子：
64.8
作者：
Sudmant PH;Rausch T;Gardner EJ;Handsaker RE;Abyzov A;Huddleston J;Zhang Y;Ye K;Jun G;Fritz MH;Konkel MK;Malhotra A;Stütz AM;Shi X;Casale FP;Chen J;Hormozdiari F;Dayama G;Chen K;Malig M;Chaisson MJP;Walter K;Meiers S;Kashin S;Garrison E;Auton A;Lam HYK;Mu XJ;Alkan C;Antaki D;Bae T;Cerveira E;Chines P;Chong Z;Clarke L;Dal E;Ding L;Emery S;Fan X;Gujral M;Kahveci F;Kidd JM;Kong Y;Lameijer EW;McCarthy S;Flicek P;Gibbs RA;Marth G;Mason CE;Menelaou A;Muzny DM;Nelson BJ;Noor A;Parrish NF;Pendleton M;Quitadamo A;Raeder B;Schadt EE;Romanovitch M;Schlattl A;Sebra R;Shabalin AA;Untergasser A;Walker JA;Wang M;Yu F;Zhang C;Zhang J;Zheng-Bradley X;Zhou W;Zichner T;Sebat J;Batzer MA;McCarroll SA;1000 Genomes Project Consortium;Mills RE;Gerstein MB;Bashir A;Stegle O;Devine SE;Lee C;Eichler EE;Korbel JO
通讯作者：
Korbel JO
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
9.8
作者：
Zook JM;Catoe D;McDaniel J;Vang L;Spies N;Sidow A;Weng Z;Liu Y;Mason CE;Alexander N;Henaff E;McIntyre AB;Chandramohan D;Chen F;Jaeger E;Moshrefi A;Pham K;Stedman W;Liang T;Saghbini M;Dzakula Z;Hastie A;Cao H;Deikus G;Schadt E;Sebra R;Bashir A;Truty RM;Chang CC;Gulbahce N;Zhao K;Ghosh S;Hyland F;Fu Y;Chaisson M;Xiao C;Trow J;Sherry ST;Zaranek AW;Ball M;Bobe J;Estep P;Church GM;Marks P;Kyriazopoulou-Panagiotopoulou S;Zheng GX;Schnall-Levin M;Ordonez HS;Mudivarti PA;Giorda K;Sheng Y;Rypdal KB;Salit M
通讯作者：
Salit M
影响因子：
5.8
作者：
Anders, Simon
通讯作者：
Anders, Simon