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

use 'Genome in a Bottle' data ? http://jimb.stanford.edu/giab/

e.g: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/
