Difference between revisions of "2017 Sep Taeyoung Lab note"
From Crop Genomics Lab.
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==Fst== | ==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 | 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$V1))+geom_point()+scale_colour_manual(breaks=c('Blue','Navy'),values=c("royalblue","midnightblue")) | ||
==Tajima's D== | ==Tajima's D== |
Revision as of 07:09, 15 September 2017
Contents |
Fst
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000
Fst ploting
ggplot(data,aes(x=data$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