Hi all stars,
Given a SNP, I want to define the LD interval that the SNP locates. My far purpose is to calculate the RTC score for eQTL SNPs. Basically, I have two ideas:
- Based on the recombination hotspots, the region between two hotspots can be defined as LD intervals, like the intervals used in QTLtools (link). But the question is when the SNP overlaps with no intervals, can we say this SNP is not in LD region?
- Based on 1000G genotype data, we can use plink to calculate R2 between this SNP and surrounding SNPs. Using a solid threshold, like R2 >= 0.4, we can find the boarder of the SNP's LD interval.
Which of the two methods makes more sense? or if there is other better methods?