Second-generation PLINK: rising to the challenge of larger and richer datasets.
Second-generation PLINK: rising to the challenge of larger and richer datasets.
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DOI：
10.1186/s13742-015-0047-8
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发表时间：
2015
期刊：
影响因子：
9.2
通讯作者：
Lee JJ
中科院分区：
文献类型：
--
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
PLINK 1是一个广泛使用的开源C/C++工具集，用于全基因组关联研究（GWAS）和群体遗传学研究。然而，来自插补和全基因组测序研究的数据的稳定积累暴露了对关键功能的更快和可扩展的实现的强烈需求，例如逻辑回归、连锁不平衡估计和基因组距离评估。此外，GWAS和群体遗传数据现在经常包含基因型可能性，相位信息和/或多等位基因变异，其中没有一个可以由PLINK 1的主要数据格式表示。为了解决这些问题，我们正在为PLINK开发第二代代码库。这个代码库的第一个主要版本PLINK 1.9，引入了比特级并行的广泛使用，时间/恒定空间Hardy-Weinberg平衡和Fisher精确测试，以及许多其他算法改进。结合起来，这些变化使大多数操作加速了1-4个数量级，并允许程序处理太大而无法容纳在RAM中的数据集。我们还开发了数据格式的扩展，增加了对基因型可能性、相位、多等位基因变异和参考与替代等位基因的低开销支持，这是我们计划的第二个版本（PLINK 2.0）的基础。PLINK的第二代版本将在性能和兼容性方面提供显着的改进。这是第一次，无法访问高端计算资源的用户可以对即将投入使用的功能丰富且非常大的遗传数据集进行几项基本分析。本文的在线版本（doi：10.1186/s13742-015-0047-8）包含补充材料，可供授权用户使用。
PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1’s primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, -time/constant-space Hardy-Weinberg equilibrium and Fisher’s exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use. The online version of this article (doi:10.1186/s13742-015-0047-8) contains supplementary material, which is available to authorized users.
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影响因子：
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影响因子：
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发表时间：
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影响因子：
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