Difference between revisions of "2017 Sep Taeyoung Lab note"

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(Created page with "===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 1...")
 
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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
  
===Tajima's D===
+
====Tajima's D====
 
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000
 
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000
  
===Pi ===
+
====Pi ====
 
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000
 
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000

Revision as of 06:34, 12 September 2017

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

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