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
•
written
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Sharon
1 answer
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.
Hello, I have a similar situation to the original poster and get similar values for the relatedness_phi for the pairs in my family. In the example above, p1 and p3 have a phi of 0.287, indicating they are first degree relatives, but they are presumably unrelated. I get a similar phi when I run relatedness2 on two members of unrelated families. Any suggestions on how to fix this problem?
Try running tools on only 'PASS' variants maybe then you would see a difference.
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If the RELATEDNESS_PHI values
p2 vs p1 = 0.32219 p2 vs p3 = 0.329423 confirm the parent-offspring relationship, what about p3 vs p1 = 0.287081 are mum and dad siblings?