I am working on whole exome sequencing data, and to annotate the resulting VCF files, I have been using wANNOVAR. However, we are now going to be receiving around 1000 unannotated VCF files from our collaborator, and the disadvantage of using wANNOVAR is that one can submit only two files at a time from one IP address. I was therefore wondering if I can annotate them offline, and bedtools, as I understand is my answer to it.
My questions are -
What additional bed files will I need to annotate the variants (I am aligning my reads to hg38)?
Where can I find those files?
Is it possible for me to generate the files using hg38.fa? If yes, how?