Difference between revisions of "2017 Sep Taeyoung Lab note"
From Crop Genomics Lab.
(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...") |
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
