Genome diversity

We have included a suite of tools including pedigree analysis and variation between varieties. These tools can be useful in re-sequencing projects aiming at study of genome diversity.

Tip

Download the test dataset here.

Pedigree analysis

One basis analysis is to visualize pedigrees between varieties that illustrate breeding history. The pedigree information can be encoded in a standard .ped file.

#Family ID	Individual ID	Paternal ID	Maternal ID	Sex (1=male; 2=female; other=unknown)	Phenotype	
F001	Variety10	Variety11	Variety12	0	0
F001	Variety8	Variety9	Variety10	0	0
F001	Variety7	Variety9	Variety9	0	0
F001	Variety4	Variety7	Variety8	0	0
F001	Variety2	Variety6	Variety4	0	0
F001	Variety3	Variety4	Variety5	0	0
F001	Variety1	Variety2	Variety3	0	0

We can then easily visualize it.

The root nodes (nodes with no parent information) are assumed to be outcrossing. We can then estimate the parentage in the form of piecharts colored by the root nodes. The inbreeding coefficients ($F$) can also be estimated where there is inbreeding.

CNV between varieties