I am calculating the R2 of SNPs from 1000G phase 3 vcf files.
I first converted vcf to bed, and used R2 command. But I found some discrepancy of my results from the results on LD link, an online tool to calculate LD based on 1000G phase 3. The reason I calculated myself is I need a full LD table for all available SNPs from 1000G.
Both rs138281 and rs138285 are in the bed file, but they are not in LD. No R2 was returned by R2 command. I did not set a R2 cutoff, so it should returl all R2.
plink --bfile chr22_1000Gphase3_EUR_snp_maf_rmvsnp --r2 --out chr22_1000Gphase3_EUR_ldtable
However, they are highly correlated according to LD link (R2=0.9413 among EUR population)
Does anyone have an idea what might go wrong?