1000G LD constructed using PLINK does not match haploreg

Question

[w.denhollander]

Hi there,

I'm trying to get LD blocks from the 1000G data, and after some searching on the internet I found the genotype data and used PLINK to calculate the LD structure. However, the results do not match haploreg (http://www.broadinstitute.org/mammals/haploreg/haploreg_v3.php), which is, as far as I know, used on the same data.

[Giovanni M Dall'Olio]

It would be easier to answer you if you can give us some more information. To which of the 1000Genomes phases are you referring to? How did you calculate the LD structure? Did you use any filter? Where did you get the output of haploreg? Can you make an example of region where the two maps differ?