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背景
Plink是一个免费、开源的全基因组关联分析工具集，用于执行基本范围的、大规模分析计算的有效方式。PLINK的重点是对基因型/表型数据的分析，因此不支持此前的步骤（例如，研究设计和计划，从原始数据生成基因型或CNV调用）。通过与gPLINK和Haploview集成，可以为后续的可视化，注释和结果存储提供支持。
plink的主要功能：数据处理，质量控制的基本统计，群体分层分析，单位点的基本关联分析，家系数据的传递不平衡检验，多点连锁分析，单倍体关联分析，拷贝数变异分析，Meta分析等等。
Data management数据管理
- Read data in a variety of formats
- Recode and reorder files
- Merge two or more files
- Extracts subsets (SNPs or individuals)
- Flip strand of SNPs
- Compress data in a binary file format
Summary statistics for quality control质量控制的摘要统计
- Allele, genotypes frequencies, HWE tests
- Missing genotype rates
- Inbreeding, IBS and IBD statistics for individuals and pairs of individuals
- non-Mendelian transmission in family data
- Sex checks based on X chromosome SNPs
- Tests of non-random genotyping failure
Population stratification detection人口分层检测
- Complete linkage hierarchical clustering
- Handles virtually unlimited numbers of SNPs
- Multidimensional scaling analysis to visualise substructure
- Significance test for whether two individuals belong to the same population
- Constrain cluster solution by phenotype, cluster size and/or external matching criteria
- Perform subsequent association analyses conditional on cluster solution
Basic association testing基本关联测试
- Case/control
Standard allelic test
Fisher's exact test
Cochran-Armitage trend test
Mantel-Haenszel and Breslow-Day tests for stratified samples
Dominant/recessive and general models
Model comparison tests (e.g. general versus multiplicative) - Family-based association (TDT, sibship tests)
- Quantitative traits, association and interaction
- Association conditional on one or more SNPs
- Asymptotic and empirical p-values
- Flexible clustered permutation scheme
- Analysis of genotype probability data and fractional allele coounts (post-imputation)
Multimarker predictors, haplotypic tests多标记预测因子，单倍型测试
- Suite of flexible, conditional haplotype tests
- Case/control and TDT association on the probabilistic haplotype phase
- A set of proxy associaiton" methods to study single SNP associations in their local haplotypic context
- Imputation heuristic, to test untyped SNPs given a reference panel
Copy number variant analysis拷贝数变异分析
- Joint SNP and CNV tests for common copy number variants
- Filtering and summary procedures for segmental (rare) CNV data
- Case/control comparison tests for global CNV properties
- Permutation-based association procedure for identifying specific loci
Additional tests其他测试
- Gene-based tests of association
- Screen for epistasis
- Gene-environment interaction with continuous and dichotomous environments
Meta-analysisMeta分析
- Automatically combine several generically-formatted summary files, for millions of SNPs
- Fixed and random effects models
Result annotation and reporting结果注释和报告
- Post-analysis annotation of result files
- LD-based and region-based grouping of results across multiple studies
Additional features附加功能
- Extensible with via R function plug-ins
- Web-based SNP and gene annotation lookup feature
- Simple SNP simulation feature
- ID helper tools, for tracking and working with project data
- See the main documentation for full list of features
参考：http://zzz.bwh.harvard.edu/plink/index.shtml
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