I was wondering if anybody could share with me a working script to perform (standard) variant qc and annotation based on a vcf file?
Even if only some standard commands for annotation of exonic function, frequencies in GnomAD, and funtional predictions scores with VEP would be very helpful.
Any any additional setuo needed to incorporate external annotation databases.
maybe worth looking at the gnomad scripts? https://github.com/macarthur-lab/gnomad_hail
I don’t think anybody has stuff especially pre-boxed and ready to go, though