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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