What are the typical IBD PIHAT values calculated by PLINK for duplicate samples?

Question

[anp375]

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.

Answer 1

[MAPK]

IBD values are normally, identical samples/duplicate =1.0, 1st degree=0.5 and goes on decreasing by 1/2 for successive generation. Duplicate sample should be same as monozygotic twins in this case. Anything in between accounts for cryptic relatedness or if you have cross sample contaminations, even the duplicate samples start to show cryptic relatedness (i.e. IBD values anywhere in between relatedness). Also, plink however is widely used for kinship determination, there are several flaws.

[anp375]

I don't understand what cryptic relatedness has to do with this. Right now, I assume that the differences arise from how PLINK handled missing genotypes in the data and how indels were called differently in the two sequencing sets.