Hello everyone! I have a question regarding KING tool results. I have an SNP genotyping results of sheep species and I would like to find out kinship inference between them, specifically, I would like to reveal parent-offspring pairs. I tried to run KING with following command:
king --related --degree 3 --sexchr 27 -b plink_res.bed
As the output, I got some statistics with inferred relationship type and there were 33 pairs of parent-offspring status. However, I tried also to check it with different degrees parameter and found out that the same command but with --degree 4, --degree 5 gave me 37 parent-offspring pairs. More surprisingly was that with --degree 2 it was also 37 pairs of PO type.
Moreover, I explored the result using the command:
king --degree 3 -b plink_res.bed
and it showed 37 pairs. Seems like the specification of the sex chromosome number the source of the problem.
If I am not mistaken the --degree parameter influence kinship coefficient and it should be work like this: the bigger degree the smaller kinship coefficient and less numbers of highly related pairs. Namely, for --degree 2 output with kinship >= 0.08839, for --degree 3 output with kinship >= 0.04419, --degree 4 output with kinship >= 0.0221. Can anyone tell me please why KING's behaviour is like this? Why it works strangely in combination with --degree 3 and --sex chr 27 parameters?
