Snagger: a user-friendly program for incorporating additional information for tagSNP selection.
Snagger: a user-friendly program for incorporating additional information for tagSNP selection.
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Snagger：一个用户友好的程序，用于合并用于TAGSNP选择的其他信息。
DOI：
10.1186/1471-2105-9-174
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发表时间：
2008-03-27
影响因子：
3
通讯作者：
Conti, David V.
中科院分区：
文献类型：
--
作者：
Edlund, Christopher K.;Lee, Won H.;Li, Dalin;Van Den Berg, David J.;Conti, David V.
人们付出了相当大的努力来开发标记单核苷酸多态性 (SNP) 的有效程序。许多这些程序没有考虑到由于基因分型失败而可能导致的基因组覆盖率降低，也没有根据功能优先选择 SNP，而这可能更具有生物学重要性。我们开发了一个用户友好且高效的软件程序 Snagger，作为现有开源软件 Haploview 的扩展，它利用单核苷酸多态性 (SNP) 之间的成对 r2 连锁不平衡来选择 tagSNP。 Snagger 与包括 Tagger 在内的现有 SNP 选择算法不同，它提供的用户选项允许：(1) 基于某些特征（包括特定于平台的设计分数、功能（即编码状态）和染色体位置）对 tagSNP 进行优先级排序，(2) 跨多个群体有效选择 SNP，(3) 选择定义的基因组区域之外的 tagSNP，以提高覆盖率和基因分型成功率，以及 (4) 挑选替代 tagSNP作为 tagSNP 的备份，其故障将导致大量数据丢失。使用来自 10 个 ENCODE 区域的 HapMap 基因型数据和 Illumina 平台的设计分数，我们显示了相似的覆盖范围和设计分数分布，以及与 Web 服务器 Tagger 相比，Snagger 选择的总 tagSNP 更少。 Snagger 改进了当前可用的 tagSNP 软件包，为研究人员提供了一种选择 tagSNP 的方法，这些 tagSNP 能够可靠地捕获跨多个群体的遗传变异，同时考虑到显着的基因分型失败风险并优先考虑 SNP 特定特征。
There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important. We have developed a user-friendly and efficient software program, Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise r2 linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs. Snagger distinguishes itself from existing SNP selection algorithms, including Tagger, by providing user options that allow for: (1) prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e., coding status), and chromosomal position, (2) efficient selection of SNPs across multiple populations, (3) selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success, and (4) picking of surrogate tagSNPs that serve as backups for tagSNPs whose failure would result in a significant loss of data. Using HapMap genotype data from ten ENCODE regions and design scores for the Illumina platform, we show similar coverage and design score distribution and fewer total tagSNPs selected by Snagger compared to the web server Tagger. Snagger improves upon current available tagSNP software packages by providing a means for researchers to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
3
作者：
Ding K;Zhang J;Zhou K;Shen Y;Zhang X
通讯作者：
Zhang X
影响因子：
30.8
作者：
de Bakker, PIW;Yelensky, R;Altshuler, D
通讯作者：
Altshuler, D
影响因子：
3
作者：
Huang, YT;Zhang, K;Chao, KM
通讯作者：
Chao, KM
DOI：
10.1142/9781860948732_0011
发表时间：
2007-01-01
期刊：
Computational systems bioinformatics. Computational Systems Bioinformatics Conference
影响因子：
--
作者：
Liu, Lan;Wu, Yonghui;Jiang, Tao
通讯作者：
Jiang, Tao