Hi,

I was using annovar to do annotation and was preparing files for rare variant tests using regenie. I have 2 questions wan to ask.

1. regenie step2 for burden test requires a set list which needs gene (start) position. How do I get this gene position? Can I get it from annovar? I did not see this information from my annovar output and am really confused. Or can I use the position from a variant which belongs to this gene for this set list file?
2. In annovar annotation output, I noticed 'None' in Gene.refGene (e.g., "NONE;DDX11L1") column for intergenic. How to understand/deal with that "NONE"? Can I treat this "NONE;DDX11L1" as "DDX11L1"?

Thanks very much!