I'm working with make_snp_file.py in preparation for a burden test. I want to include coding variants with both 'HIGH' and 'MODERATE' impact based on VEP annotation. When I use --includevep "IMPACT[=]HIGH" --includevep "IMPACT[=]MODERATE" I get an empty file. I'm guessing this is because I am looking for variants that are both HIGH and MODERATE impact (mutually exclusive categories) as opposed to HIGH or MODERATE. Is there a way to specify 'or' so as to include both categories? I'm imagining something like --includevep "IMPACT[=]HIGH[|]IMPACT[=]MODERATE" . Thanks for developing TRAPD and thanks for your help.
I'm working with make_snp_file.py in preparation for a burden test. I want to include coding variants with both 'HIGH' and 'MODERATE' impact based on VEP annotation. When I use --includevep "IMPACT[=]HIGH" --includevep "IMPACT[=]MODERATE" I get an empty file. I'm guessing this is because I am looking for variants that are both HIGH and MODERATE impact (mutually exclusive categories) as opposed to HIGH or MODERATE. Is there a way to specify 'or' so as to include both categories? I'm imagining something like --includevep "IMPACT[=]HIGH[|]IMPACT[=]MODERATE" . Thanks for developing TRAPD and thanks for your help.