vcftools --fst-window- problems

Question

[florycamacho305]

Hi all,

I'm using vcftools to calculate fst :

vcftools --vcf file.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out pop1_pop2.FST

which works. However, when I'm trying to slide it by windows, my code doesn't work.

vcftools --vcf file.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --fst-window-size 1000 --fst-window-step 1000 --out pop1_pop2.1000.FST

I have used the same codes with other vcf file and both worked.

Is this problem related to the vcf file? or I have to look for the right window size?

I hope you can help me,

Thanks

Answer 1

[fu_entomology]

I am having similar issues here. What was your error message? If you remove --fst-window-step 1000, it might work.