General question regarding WES analysis

Question

[psmirin]

Hi,

I got a general question regarding WES analysis, I got hundreds of samples (many different families with different diseases) on which I have run GATK and the SnpEff & SnpSift using their db: clinvar, dbSNP& Exac, in order to filter the disease causing variants in patients. I want to filter the variants on those criteria:

1. Known mutation - clinvar/(HGMD- is there an option to add this db too?)
2. Known genes – How and where from can I extract this data?
3. Severe mutation – based on SnpEff ranking (high, moderate, low)
4. New genes - How can I extract this data?
5. Private variants in a family – based on the other variants patients data

Is this the right way to handle those criteria? how can I approach number 2&4?

Thanks alot