Question: vcftool negative relatedness values for family members
0
gravatar for marcusanaymik
3.9 years ago by
United States
marcusanaymik10 wrote:

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 qc kinship pedigree • 1.5k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 3.9 years ago by marcusanaymik10

Hi Marcus,

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

Thanks,

Caragh

ADD REPLYlink written 2.1 years ago by Caragh 40

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.

ADD REPLYlink written 21 days ago by gmeeks32810
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1719 users visited in the last hour