vcftool negative relatedness values for family members

Question

[marcusanaymik]

I have ran the vcftools relatedness2 analysis on a few families data and some families produce positive relatedness phi scores and some families produce negative phi scores. In the range of + or - [0.1 - 0.3] for child-parents. Is the + - irrelevant?

[Caragh]

Hi Marcus,

Did you ever find out if the + - is irrelavent? I'm wondering the same thing!

Thanks,

Caragh

[gmeeks328]

If anyone is still looking, there's a good, quick comparison between --relatedness and --relatedness2 in this post. I just ran into the negative relatedness phi issue in my analysis, which is addressed in the KING inference page specified in the post I linked. Per the KING tutorial listed above,

A negative kinship coefficient estimation indicates an unrelated relationship. The reason that a negative kinship coefficient is not set to zero is a very negative value may indicate the population structure between the two individuals.