I am trying to exactly understand how LD score is computed in GCTA.
As described in the documentation, the genome is chopped into segments with length of L for LD calculation. Two adjacent segments are overlapped. The size of the overlap is L/2.
Here come my questions:
The starting position of the genome corresponds to the 0 base-pair or to the position of the first SNP in the dataset?
How LD score is computed for a given SNP that is contained in both adjacent segments? That is, imagine that I have a genome of 2 Mb and I set a window size of 1 Mb. According to what I understood, we will get 3 segments with interval boundaries at positions: segment1) 0Mb - 1Mb; segment2) 0.5Mb - 1.5Mb; and segment3) 1Mb - 2Mb. So what the program does with a SNP (let's call it SNP X),for instance, at position 0.7Mb, that thus fall within both segment1 and segment2? Does GCTA compute the LD score of the SNP X considering only the sites within segment1, only the sites within segment2 or both?
Hi all,
I am trying to exactly understand how LD score is computed in GCTA. As described in the documentation, the genome is chopped into segments with length of L for LD calculation. Two adjacent segments are overlapped. The size of the overlap is L/2.
Here come my questions:
The starting position of the genome corresponds to the 0 base-pair or to the position of the first SNP in the dataset?
How LD score is computed for a given SNP that is contained in both adjacent segments? That is, imagine that I have a genome of 2 Mb and I set a window size of 1 Mb. According to what I understood, we will get 3 segments with interval boundaries at positions: segment1) 0Mb - 1Mb; segment2) 0.5Mb - 1.5Mb; and segment3) 1Mb - 2Mb. So what the program does with a SNP (let's call it SNP X),for instance, at position 0.7Mb, that thus fall within both segment1 and segment2? Does GCTA compute the LD score of the SNP X considering only the sites within segment1, only the sites within segment2 or both?
Thank you in advance, Gabriele