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