Hey, 

I have to do some variant calling in a plant organism (diploid)

I have selected the programs I want to test before I use my own data. (Freebayes, Samtools, SOAPsnp and Cortex_VAR.)
However i am struggling to come up with a reference to compare the tools against.
First i want to test the software before i can use it on my own data.

Is there a benchmark i can use or is it better to simulate my own reference? and use the tools accordantly 
 
Regards,
Covux

There are a few public reference genomes listed here: http://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/genomic_data_toc.html
