Relatedness vs relatedness2 from vcftools give different results

Relatedness vs relatedness2 from vcftools give different results

1

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


Relatedness


Kinship

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