2017 Sep Taeyoung Lab note

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Contents

Fst

vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000

Fst ploting

ggplot(data,aes(x=data$V2,y=data$V3,colour=data$V1))+geom_point()+scale_colour_manual(breaks=c('Blue','Navy'),values=c("royalblue","midnightblue"))

Tajima's D

vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000

Pi

vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000