Software for the analysis of large-scale genotyping and sequencing studies

描述(由申请人提供)：本项目的目标是在现有的软件包PLINK及其配套软件包PLINK/SEQ的基础上，开发用于分析大规模基因分型和测序研究的数据的软件。旨在操纵和分析全基因组SNP数据集的PLINK已经积极开发了六年多，拥有广泛的用户基础，在同行评议的期刊上有超过5000篇引用。在过去的几年里，我们为大型稀有变异数据集的分析增加了相当多的支持，主要集中在PLINK/SEQ中的整个外显子组测序研究。在这一更新申请中，我们寻求1)在PLINK和PLINK/SEQ之间提供更紧密的整合，目的是为全基因组关联和测序研究提供一个单一界面，特别是在大型统计推算数据集的背景下；2)加强现有的数据集成设施，跨越不同类别的遗传变异以及大型、多样化的数据集；3)改进对基于家族的数据集的处理，侧重于(核)基于家族的关联研究中的从头开始和遗传变异；4)致力于改进超大型数据集的性能。将特别注意确保与更广泛的遗传学社区产生的其他主要软件、文件格式和资源的互操作性。

DESCRIPTION (provided by applicant): The objective of this project is to develop software for the analysis of data from large-scale genotyping and sequencing studies, building on the existing software package PLINK and its companion package PLINK/Seq. Designed to manipulate and analyze whole-genome SNP datasets, PLINK has been actively developed for over six years and has a wide base of users, with over 5000 citations in peer-reviewed journals. Over the past years, we have added considerable support for the analysis of large rare variant datasets, primarily focused on whole-exome sequencing studies in PLINK/Seq. In this renewal application, we seek to 1) provide tighter integration between PLINK and PLINK/Seq, aiming to provide a single interface for both genome-wide association and sequencing studies, particularly in the context of large statistically-imputed datasets; 2) enhance the data-integration facilities already present, across different classes of genetic variation as well as large, diverse datasets; 3) provide improved handling of family-based datasets, focused on de novo and inherited variation in (nuclear) family-based association studies; 4) to work on improving performance on very large datasets. Particular attention will be paid to ensure interoperability with other major software, file-formats and resources that are generated by the broader genetics community.