I have a couple of questions regarding the Varscan 2 output/options. The first is regarding the --min-coverage option. I used the following:
--mpileup 1 --tumor-purity 1 --min-coverage 20 --min-var-freq 0.01 --somatic-p-value 0.00001
I was expecting to see variants only called in the tumour only if they were 20 reads over that bp/indel. As I am not seeing this using --min-coverage 20, could someone explain to me what this option means? And what is the best method to determine if a variant is real or not?
We have fresh frozen tumor with matched normal that we sequenced to a depth of ~100x. Are there other parameters I should take into consideration too? We are comparing two different subtypes (invasive and non-invasive) and would like to identify those variants that are transmitted between these two groups.