**8.2k**wrote:

Hi colleagues,

Just very simple question. When we calculate LD, we need P(A),P(a),P(B),P(b) and then

```
D=P(AB)-P(A)P(B)
r=P(AB)-P(A)P(B)/sqrt(P(A)P(a)P(B)P(b))
```

However, for raw SNPs or mutation, P(A) or P(B) might be 0. In such situation, r can not be calculated. Is there any compromised way to calculate r or D' for such situation?

In another way, suppose I only observe 1 haplotype for 2 loci in all the samples (very large samples)? Can I take the such as as completed linkage or I can take record LD as 'NA'?

Thanks

**20**• written 4.1 years ago by Shicheng Guo •

**8.2k**