Varscan for SNP calling from pooled RNA seq data

Question

[hpapoli]

Hello,

I need to call SNPs from pooled-RNA seq data. I want to use FreeBayes, GATK and Varscan. For VarScan, they say that one needs to set the min coverage, min variant frequency and p-value. It is rather complicated to set these values. I was wondering if anyone has any experience with this?

Thanks,

Homa