This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.
Are you keeping a version of your scripts with old columns names
or the scripts need an update ?
In the below line, the column name 'aaf_gnomad_genome_all' should be replaced with :
--filter "(aaf_gnomAD_genome_all <= 0.01) and (confidentregion = 1) and (inhousedb_ac <= 3 or inhousedb_ac is NULL) and (impact_severity == 'HIGH' or impact_severity=='MED')" \