Genetic distance calculation

[John Riascos]

Hello everyone,

I am trying to understand how genetic distance is calculated in Tassel. I am new to the SNP world, and in my previous work with SSR, when performing genetic diversity analyses, it always was important to use the right genetic distance coefficient (mostly we used Nei´s coefficient). I know how to generate a genetic distance matrix in Tassel 5, however, I need to know how is it calculated. Your help is appreciated. Thanks!

John

[Tony Travis]

On 01/04/15 16:02, John Riascos wrote:

Hello everyone,

I am trying to understand how genetic distance is calculated in Tassel. I am new to the SNP world, and in my previous work with SSR, when performing genetic diversity analyses, it always was important to use the right genetic distance coefficient (mostly we used Nei´s coefficient). I know how to generate a genetic distance matrix in Tassel 5, however, I need to know how is it calculated. Your help is appreciated. Thanks!

Hi, John.

Michele Jorge and I asked the same question a while ago - Peter Bradbury answered:

TASSEL calculates distance as 1 - IBS (identity by state) similarity, with IBS defined as the probability that alleles drawn at random from two individuals at the same locus are the same. For clustering, the distance of an individual from itself is set to 0. 

The calculation is based on the definition. For a bi-allelic locus with alleles A and B, probabilityIBS(AA,AA) = 1, pIBS(AA,BB) = 0, pIBS(AB, xx) = 0.5, where xx is any other genotype. For two taxa, pIBS is averaged over all non-missing loci. Distance is 1 - pIBS. The kinship calculation is related but different and is described in Endelman and Jannink (2012) Shrinkage Estimation of the Realized Relationship Matrix. G3 2:1405-1413, using the non-shrunk version under the assumption that generally, number of markers > number of individuals.

HTH,

  Tony.

[John Riascos]

Thanks Tony. Truly helpful!

John

[Terry Casstevens]

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/DistanceMatrix/DistanceMatrix

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[John Riascos]

Thanks Terry. I can check the Wiki now for other questions.

John

On Wednesday, 1 April 2015 10:02:00 UTC-5, John Riascos wrote: