EMMAX - kinship matrix

[jw...@nd.edu]

Hi, I tried EMMAX to create a kinship matrix, but only NaN appears in the matrix. I set MAF threshold as 1%, and my vcf file is filtered through GATK 10x coverage with 75% samples. FYI, this is RAD-seq data with 4 populations, total 51 individuals. Any further suggestion I can try? Thank you!

[Hyun Min Kang]

There is call rate threshold you can apply, and you need to use larger frequency threshold such as 5% if the sample size is that small

On Fri, Apr 3, 2015, 1:51 PM  <jw...@nd.edu> wrote:

Hi, I tried EMMAX to create a kinship matrix, but only NaN appears in the matrix. I set MAF threshold as 1%, and my vcf file is filtered through GATK 10x coverage with 75% samples. FYI, this is RAD-seq data with 4 populations, total 51 individuals. Any further suggestion I can try? Thank you!

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