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vcftool negative relatedness values for family members

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?

vcftools kinship qc pedigree
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updated by Biostar Biostar • written by marcusanaymik • marcusanaymik

Hi Marcus,

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

Thanks,

Caragh

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written by Caragh • Caragh

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.

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written by gmeeks328 • gmeeks328

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