4.14 Conclusion

In this lab, we used genotype data from the 1000 Genomes Project to ask whether there is linkage disequilibrium between two SNPs on chr21.

Using data from the VCF, we used table to count how often we observe combinations of alleles at these SNPs.
We used the data in the table to calculate three LD statistics:
- \(\mathbf{D}\): the deviation of the observed haplotype frequency from the expected haplotype frequency
- \(\mathbf{D'}\): a normalization of \(D\) that ranges from \([-1, 1]\)
- \(\mathbf{r^2}\): how well the allele at one locus predicts the allele at another locus
We used LDlink to visualize how blocks of LD define haplotypes.