I want to do variant calling from RNA-seq and I've followed GATK instruction at https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 and obtained the VCFs, one for a drug-sensitive cell line, the other for drug resistance cell line.
Now I want to
1) Find all those "meaningful" (e.g. indels, non-synonymous mutations) variants in each cell line, or at least sort the variants in terms of likely severity (e.g. rank importance of indels > missense/nonsense > synonymous > intergenic mutations) or validated clinical implications?
2) Find all those variants occur in the drug resistance cell line but not in the drug sensitive cell line, or vice versa, and rank these variants as stated in 1).
What are the best tools to do this?