Question: Calculate Fst to draw Manhattan plot

1

mostafarafiepour •

**60**wrote:Hi All,

I trying to calculate Fst. In the first step, I used the following script to calculate Fst with window 100 kb

```
./vcftools --vcf input_data.vcf --weir-fst-pop population_1.txt --weir-fst-pop population_2.txt --fst-window-size 100000 --fst-window-step 50000 --out pop1_vs_pop2
```

But in the next step, I do not know how to convert the output file to z-transform? Because before plotting the plot using the Manhattan package in R, z-transform must be performed.

Best Regard

Mostafa

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modified 7 months ago
by
RamRS ♦

**21k**• written 7 months ago by mostafarafiepour •**60**
Maybe this link is relevant, http://membres-timc.imag.fr/Olivier.Francois/LEA/files/LEA_snmf.html

7.1kmany thanks for your reply,

This is the output of the Fst stage:

I do not know exactly which of these columns should be z-transformed and how?

60