Difference between revisions of "2017 Sep Taeyoung Lab note"

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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