I want to check for concordance in two different sequencing datasets. One is whole exome sequencing and the other is whole genome sequencing. 6 samples were sequenced in both sets.
The PLINK IBD calculation for the duplicate samples gives pairwise PIHAT values above 0.5 (first degree relatedness), but they're not close to 1(twins or duplicate). They're mostly around 0.75 - 0.85. I want to make sure these values are normal.