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:
- Known mutation - clinvar/(HGMD- is there an option to add this db too?)
- Known genes – How and where from can I extract this data?
- Severe mutation – based on SnpEff ranking (high, moderate, low)
- New genes - How can I extract this data?
- 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?