从fastq到群体结构分析软件及使用方法

比对分析

1. bwa

2. 排序，因为后续处理都需要按照基因组顺序进行排序

3. 进行捕获数据的提取和统计

6. 去除重复区域

7. 统计深度信息

1. 建立索引

变异检测

1. gatk进行单个样品gvcf检测

2. 合并gvcf

3. call 基因型

4. 拆分snp，indel

5. 进行基础质量过滤

6. 进行标记群体质量过滤

##　群体结构分析

1. 数据格式转化

2. PCA分析

3. TREE 分析

4. STRUCTURE分析

软件文献

• [1] Li, H. and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009. 25(14): p. 1754-60.
• [2] Li, H., et al., The Sequence Alignment/Map format and SAMtools.Bioinformatics, 2009. 25(16): p. 2078-9.
• [3] Danecek, P., et al., The variant call format and VCFtools. Bioinformatics, 2011. 27(15): p. 2156-8.
• [4] Purcell, S., et al., PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 2007. 81(3): p. 559-75.
• [5] Yang, J., et al., GCTA: A Tool for Genome-wide Complex Trait Analysis. The American Journal of Human Genetics, 2011. 88(1): p. 76-82.
• [6] Alexander, D.H., J. Novembre, and K. Lange, Fast model-based estimation of ancestry in unrelated individuals. Genome Res, 2009. 19(9): p. 1655-64.
• [7] Vilella, A.J., et al., EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res, 2009. 19(2): p. 327-35.