Question: Relatedness vs relatedness2 from vcftools give different results
0
gravatar for Sharon
15 months ago by
Sharon420
Sharon420 wrote:

Hello All How to you think about this relatedness results?

When I use relatedness2 in vcftools I got this:

vcftools --gzvcf p123.vcf.gz --relatedness2 

INDV1   INDV2   N_AaAa  N_AAaa  N1_Aa   N2_Aa   RELATEDNESS_PHI
p1      p1      47388   0       47388   47388   0.5
p1      p2      28084   0       47388   39778   0.32219
p1      p3      27242   0       47388   47505   0.287081
p2      p1      28084   0       39778   47388   0.32219
p2      p2      39778   0       39778   39778   0.5
p2      p3      28753   0       39778   47505   0.329423
p3      p1      27242   0       47505   47388   0.287081
p3      p2      28753   0       47505   39778   0.329423
p3      p3      47505   0       47505   47505   0.5

But when I use that relatedness in vcftools I got this:

vcftools --gzvcf p123.vcf.gz --relatedness

INDV1   INDV2   RELATEDNESS_AJK
p1      p1      0.428714
p1      p2      -0.187837
p1      p3      -0.343416
p2      p2      0.552425
p2      p3      -0.171243
p3      p3      0.423852

P2 is supposed to be the son of p3(father) and p1(mother) or this is what We wanna prove. It was not normal birth, a kind of artificial insemination

I am surprised that the PHI score between P1 and P1 , P2 AND P2 , and P3 and P3 is only 0.5 using both commands?

I understand that both command rely on different approaches. But not sure how to conclude whether or not to confirm relatedness. How do you think? If I trust the relatedness2, is 0.3 a confirmation for parent relationship?

Thanks thanks

kinship relatedness • 1.0k views
ADD COMMENTlink modified 7 weeks ago by ognjen011160 • written 15 months ago by Sharon420
1
gravatar for ognjen011
7 weeks ago by
ognjen011160
ognjen011160 wrote:

Hi!

The --relatedness method based on doi:10.1038/ng.608 is only appropriate for large cohorts. Although this is not properly indicated in the documentation, it is revealed in questions on SourceForge. Looking at the paper equation (6) in supplementary, the values of AF near 0 or 1 make the equation numerically unstable. I would just ignore this result.

The --relatedness2 method is based on the KING inference, and you have a very good tutorial here. You can interpret the relatedness_phi as the probability to find identical alleles when randomly sampling one allele from each heterozygous individual. So for one individual AB, and the parent AC, there is p=0.25 to choose A from both individuals. That probability is 0.5 when AB is compared to AB.

From the tutorial:

an estimated kinship coefficient range >0.354, [0.177, 0.354], [0.0884, 0.177] and [0.0442, 0.0884] corresponds to duplicate/MZ twin, 1st-degree, 2nd-degree, and 3rd-degree relationships respectively

Your result confirms the parent-offspring relationship, but could also mean a sibling.

ADD COMMENTlink written 7 weeks ago by ognjen011160

Great, thank you :)

ADD REPLYlink written 26 days ago by Sharon420
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