calculate kinship in SPAGeD
Entering edit mode
4.1 years ago
LJ ▴ 250

Hi all, i have a set of SNP data for some samples (diploid species), and I want to calculate the kinship using SPAGeD software.So i how do i set the SNP data form to calculate kinship? And the following data is a example data. So the first line includes(# number of individuals; #number of categories; #number of spatial coordinates; #number of SNP; # number of digit; #ploidy);

And the second line : # distance intervals.So,

Question1: i am sure that number of individuals=9,number of categories=0,number of SNP=9,ploidy=2, but what's the meaning of ("#number of spatial coordinates","# number of digit","# distance intervals")?

Question 2 How to input SNP data? which one should i choose, TT/TT,TT,or 11/11...?

Thanks in advance.

 Marker1 Marker2 Marker3 Marker4 Marker5 Marker6 Marker7 Marker8 Marker9
individual1 CC  TT  GG  TT  GG  AA  AA  CC  CC
individual2 AA  TT  GG  TT  GG  GG  AA  GG  CC
individual3 CC  TT  GG  CC  GG  AA  CC  CC  CC
individual4 AA  TT  GG  TT  GG  GG  CC  CC  TT
individual5 CC  TT  GG  TT  AA  GG  AA  CC  TT
individual6 CC  TT  GG  TT  AA  GG  AA  CC  CC
individual7 CC  TT  GG  TT  AA  GG  AA  CC  CC
individual8 AA  TT  AA  TT  GG  GG  CC  CC  CC
individual9 CC  TT  GG  TT  GG  GG  CC  GG  CC`
SNP kinship GWAS • 846 views

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