Re: [Vcftools-help] Computing Relatedness and interpreting Inbreeding

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Hello,

The relatedness statistic is based on the method of Yang et al, 2010 (doi:10.1038/ng.608). Specifically, it calculates the unadjusted Ajk statistic (equation 6 of paper). The expectation of Ajk is zero for individuals within a populations, and one for an individual with themselves. However, it assumes that the individuals in the VCF file form a reasonably large sample from a population. The equation isn't appropriate for a small sample of related individuals.

The F statistic is the inbreeding coefficient. Again, this calculation assumes a reasonably large sample from a population.

Regards,

Adam

-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
1301 Morris Park Avenue,
Price Center 320,
Bronx, New York 10461

Tel: +1 (718) 678 1038

On 15 Mar 2012, at 2:34 PM, vijai2007 wrote:

> Hi, I have two questions.
> 1)  Using the  --relatedness option, I computed relatedness of individuals in a family.
>      The pedigree shows that two of the samples here as A and B are identical twins.
> However, the output shows only  a relatedness of 0.32
> How to interpret the RELATEDNESS column, assuming that the pedigree and samples are correct.
> 
> INDV1	INDV2	RELATEDNESS
> C	C	0.926103
> D	D	0.794354
> E	E	0.769701
> F	F	0.735845
> B	B	0.717206
> A	A	0.713037
> A	B	0.324192
> F	D	-0.00740291
> F	E	-0.0592543
> E	A	-0.0967427
> E	B	-0.0969141
> F	A	-0.125153
> F	B	-0.12634
> E	D	-0.202799
> D	C	-0.22547
> A	D	-0.250855
> D	B	-0.251969
> E	C	-0.265452
> F	C	-0.290661
> B	C	-0.332576
> A	C	-0.334248
> 
> 
> 
> 2)
> I performed the "--het" analysis on 4 members of another family.
> However, I am unsure how to interpret the F statistic here.
> 
> INDV    O(HOM)  E(HOM)  N_SITES F
> Sample1       38082   40979.5 69325   -0.10222
> Sample2       36266   40979.5 70553   -0.15938
> Sample3       37258   40979.5 70505   -0.12605
> Sample4       36600   40979.5 70625   -0.14773
> 
> Thanks for reading,
> JVJ
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