关联分析-tassel笔记

1. 过滤

/gpfs01/home/jingjing/software/vcftools_0.1.12b/bin/./vcftools --vcf ../EG5.var.flt.plink.yield.vcf --min-alleles 2 --max-alleles 2 --maf 0.05 --max-missing 0.3  --minQ 20 --recode --out test

2. 计算关系矩阵

perl /gpfs01/home/jingjing/software/tassel-5-standalone/run_pipeline.pl -fork1 -Xms512m -Xmx2000g -vcf test.recode.vcf -ck -export bnapus.kinship.txt -runfork1

3. 关联分析

perl /gpfs01/home/jingjing/software/tassel-5-standalone/run_pipeline.pl -Xms512m -Xmx2000g -fork1 -vcf test.recode.vcf -fork2 -r yield_phenotype.txt -fork3 -k bnapus.kinship.txt -fork4 -q yield.population.txt -combine5 -input1 -input2 -intersect -combine6 -input5 -input3 -input4 -mlm -mlmVarCompEst P3D -mlmCompressionLevel Optimum -mlmOutputFile out -runfork1 -runfork2 -runfork3 -runfork4

phenotype 格式：

<Trait> branch  weight  average

AF01    74      582.8   7.88

AF02    58      636.5   10.97

AF03    54      529     9.8

AF04    50      499.7   9.99

AF05    48      510.3   10.63

AF06    57      497.6   8.73

AF07    58      379.7   6.55

AF08    60      509.4   8.49

AF09    54      467.6   8.66

AF10    60      483.9   8.07

C01     44      285.8   6.5

C02     57      295.1   5.18

C03     60      341     5.68

C04     57      297.1   5.21

C05     59      283.6   4.81

C06     62      309.6   4.99

C07     56      287.9   5.14

C08     35      163     4.66

population格式：

<Covariate>                    

<Trait> Q1      Q2      Q3

AF01    0.00001 0.00001 0.99998

AF02    0.00001 0.00001 0.99998

AF03    0.00001 0.00001 0.99998

AF04    0.00001 0.00001 0.99998

AF05    0.00001 0.00001 0.99998

AF06    0.00001 0.00001 0.99998

AF07    0.00001 0.00001 0.99998

AF08    0.00001 0.00001 0.99998

AF09    0.00001 0.00001 0.99998

AF10    0.00001 0.00001 0.99998

C01     0.000015        0.999975        0.00001

C02     0.00001 0.99998 0.00001

C03     0.00001 0.99998 0.00001

C04     0.00001 0.99998 0.00001

C05     0.00001 0.99998 0.00001

4. 画Manhattan图

从Tassel运行结果中提取，并转化为如下格式：

SNP     CHR     BP      P

S1_386  1       386     0.4226629180439654

S1_393  1       393     0.8793687690943273

S1_394  1       394     0.8794028337075487

S1_472  1       472     0.9933042683021722

S1_992  1       992     0.9996850282507873

S1_1184 1       1184    0.9999957326017308

S1_1221 1       1221    0.9999950334001071

S1_1409 1       1409    0.9955586559645526

S1_1415 1       1415    0.993560205062504

S1_1419 1       1419    0.9933310794947143

S1_1422 1       1422    0.9950416891292813

S1_1423 1       1423    0.9941156522473816

利用R的包来画常见的manhattan图和QQ图：

•library(qqman)

•gwasResults<-read.table(“data”)

•png("manhattan.png")

•manhattan(gwasResults, col = c(1:16), main = "Results from simulated trait")

•dev.off()

一组好的关联分析结果：

一组不好的关联分析结果：

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