SNPFile--a software library and file format for large scale association mapping and population genetics studies.
SNPFile--a software library and file format for large scale association mapping and population genetics studies.
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DOI：
10.1186/1471-2105-9-526
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发表时间：
2008-12-08
影响因子：
3
通讯作者：
Mailund, Thomas
中科院分区：
文献类型：
--
作者：
Nielsen, Jesper;Mailund, Thomas
高通量基因分型技术使成千上万的个体在成千上万的标记物中进行成本有效的分型，用于全基因组研究。数据采集技术的巨大进步使得有效地存储和操作数据成为信息学的挑战。虽然以前电子表格和文本文件是足够的解决方案，但增加的数据大小要求更有效的解决方案。我们描述了用于SNP数据的一种新的二进制文件格式，以及用于文件操作的软件库。该文件格式使用灵活的序列化机制将基因型数据与任何类型的附加数据存储在一起。该格式被设计为对大多数多位点分析方法的访问模式具有IO效率。新的文件格式对于我们自己的研究非常有用，因为它大大减少了跟踪各种辅助数据的信息学负担，并且内存和IO效率大大简化了分析运行。该文件格式的一个主要限制是，它仅由我们自己实验室开发的一组非常有限的分析工具支持。通过脚本接口，可以轻松编写与该格式之间的转换器，这在一定程度上减轻了这一点。
High-throughput genotyping technology has enabled cost effective typing of thousands of individuals in hundred of thousands of markers for use in genome wide studies. This vast improvement in data acquisition technology makes it an informatics challenge to efficiently store and manipulate the data. While spreadsheets and at text files were adequate solutions earlier, the increased data size mandates more efficient solutions. We describe a new binary file format for SNP data, together with a software library for file manipulation. The file format stores genotype data together with any kind of additional data, using a flexible serialisation mechanism. The format is designed to be IO efficient for the access patterns of most multi-locus analysis methods. The new file format has been very useful for our own studies where it has significantly reduced the informatics burden in keeping track of various secondary data, and where the memory and IO efficiency has greatly simplified analysis runs. A main limitation with the file format is that it is only supported by the very limited set of analysis tools developed in our own lab. This is somewhat alleviated by a scripting interfaces that makes it easy to write converters to and from the format.
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影响因子：
30.8
作者：
Arking, Dan E.;Pfeufer, Arne;Chakravarti, Aravinda
通讯作者：
Chakravarti, Aravinda
影响因子：
30.8
作者：
Smyth, Deborah J.;Cooper, Jason D.;Todd, John A.
通讯作者：
Todd, John A.
影响因子：
30.8
作者：
Barrett, Jeffrey C.;Cardon, Lon R.
通讯作者：
Cardon, Lon R.
影响因子：
3
作者：
Mailund, Thomas;Besenbacher, Soren;Schierup, Mikkel H.
通讯作者：
Schierup, Mikkel H.
影响因子：
64.8
作者：
Easton, Douglas F.;Pooley, Karen A.;Dunning, Alison M.;Pharoah, Paul D. P.;Thompson, Deborah;Ballinger, Dennis G.;Struewing, Jeffery P.;Morrison, Jonathan;Field, Helen;Luben, Robert;Wareham, Nicholas;Ahmed, Shahana;Healey, Catherine S.;Bowman, Richard;Meyer, Kerstin B.;Haiman, Christopher A.;Kolonel, Laurence K.;Henderson, Brian E.;Le Marchand, Loic;Brennan, Paul;Sangrajrang, Suleeporn;Gaborieau, Valerie;Odefrey, Fabrice;Shen, Chen-Yang;Wu, Pei-Ei;Wang, Hui-Chun;Eccles, Diana;Evans, D. Gareth;Peto, Julian;Fletcher, Olivia;Johnson, Nichola;Seal, Sheila;Stratton, Michael R.;Rahman, Nazneen;Chenevix-Trench, Georgia;Bojesen, Stig E.;Nordestgaard, Borge G.;Axelsson, Christen K.;Garcia-Closas, Montserrat;Brinton, Louise;Chanock, Stephen;Lissowska, Jolanta;Peplonska, Beata;Nevanlinna, Heli;Fagerholm, Rainer;Eerola, Hannaleena;Kang, Daehee;Yoo, Keun-Young;Noh, Dong-Young;Ahn, Sei-Hyun;Hunter, David J.;Hankinson, Susan E.;Cox, David G.;Hall, Per;Wedren, Sara;Liu, Jianjun;Low, Yen-Ling;Bogdanova, Natalia;Schuermann, Peter;Doerk, Thilo;Tollenaar, Rob A. E. M.;Jacobi, Catharina E.;Devilee, Peter;Klijn, Jan G. M.;Sigurdson, Alice J.;Doody, Michele M.;Alexander, Bruce H.;Zhang, Jinghui;Cox, Angela;Brock, Ian W.;MacPherson, Gordon;Reed, Malcolm W. R.;Couch, Fergus J.;Goode, Ellen L.;Olson, Janet E.;Meijers-Heijboer, Hanne;van den Ouweland, Ans;Uitterlinden, Andre;Rivadeneira, Fernando;Milne, Roger L.;Ribas, Gloria;Gonzalez-Neira, Anna;Benitez, Javier;Hopper, John L.;McCredie, Margaret;Southey, Melissa;Giles, Graham G.;Schroen, Chris;Justenhoven, Christina;Brauch, Hiltrud;Hamann, Ute;Ko, Yon-Dschun;Spurdle, Amanda B.;Beesley, Jonathan;Chen, Xiaoqing;Mannermaa, Arto;Kosma, Veli-Matti;Kataja, Vesa;Hartikainen, Jaana;Day, Nicholas E.;Cox, David R.;Ponder, Bruce A. J.
通讯作者：
Ponder, Bruce A. J.