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，后面几列为不同的性状数据：

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：

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