Question: General question regarding WES analysis
gravatar for psmirin
3.5 years ago by
psmirin0 wrote:


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

sequencing next-gen • 712 views
ADD COMMENTlink written 3.5 years ago by psmirin0
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