群体分化指数 FST

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1  Weir & Cockerham, 1984

Weir BS, Cockerham CC (1984) Evolution 38:1358-1370

1.1  一对等位基因

$$ \hat \theta  = \frac{a}{a+b+c} $$

$$ a = \frac{\bar n}{n_c} \left\{ s^2 - \frac{1}{\bar n - 1} \left[ \bar p (1 - \bar p) - \frac{r-1}{r} s^2 - \frac{1}{4} \bar h \right] \right\} $$

$$ b = \frac{\bar n}{\bar n - 1} \left[ \bar p (1 - \bar p) - \frac{r-1}{r} s^2 - \frac{2 \bar n - 1}{4 \bar n} \bar h \right] $$

$$ c = \frac{1}{2} \bar h $$

$$ \bar n = \frac{\sum{n_i}}{r} $$

$$ n_c = \frac{r \bar n - \sum{n_i^2} / r \bar n}{r-1} $$

$$ \bar p = \frac{\sum{n_i \tilde p_i}}{r \bar n} $$

$$ s^2 = \frac{\sum{n_i (\tilde p_i - \bar p)^2}}{(r-1) \bar n} $$

$$ \bar h = \frac{\sum{n_i \tilde h_i}}{r \bar n} $$

1.2  复等位基因

$$ \hat \theta  = \frac{\sum \nolimits_u a_u }{\sum \nolimits_u \left(a_u + b_u + c_u \right)} $$

1.3  多个位点

$$ \hat \theta  = \frac{\sum\nolimits_l \sum\nolimits_u a_{lu}}{\sum\nolimits_l \sum\nolimits_u \left(a_{lu} + b_{lu} + c_{lu} \right)} $$

2  Weir & Hill, 2002

Weir BS, Hill WG (2002) Annu Rev Genet 36:721-750

$$ \hat \theta _u = \frac{MSP_u - MSG_u}{MSP_u + (n_c - 1) MSG_u} $$

$$ MSP_u = \frac{1}{r - 1} \sum\limits_{i=1}^r {n_i (\tilde p_{iu} - \bar p_u)^2} $$

$$ MSG_u = \frac{1}{\sum\limits_{i=1}^r (n_i - 1)} \sum\limits_{i=1}^r n_i \tilde p_{iu} (1 - \tilde p_{iu}) $$

$$ n_c = \frac{1}{r-1} \left( \sum\limits_{i=1}^r n_i - \frac{\sum\nolimits_{i=1}^r n_i^2}{\sum\nolimits_{i=1}^r n_i} \right) = \frac{1}{r-1} \sum\limits_{i=1}^r n_{ic} $$

$$ n_{ic} = n_i - \frac{n_i^2}{\sum\nolimits_{i=1}^r n_i} $$

3  计算

Weir BS, Cockerham CC (1984) Evolution 38:1358-1370

Akey JM, et al. (2002) Genome Res 12:1805-1814

VCFtools

vcftools --vcf geno.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt
vcftools --vcf geno.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --fst-window-size 100000 --fst-window-step 25000

GCTA

gcta64 --bfile test --fst --sub-popu subpopu.txt --out test

群体分化指数 FST

标签：ann   res   too   -o   col   https   txt   计算   step   

原文地址：https://www.cnblogs.com/hjbreg/p/11827604.html