Basically, I have a lot of missing GERP scores in my annotated VCF and I don't want that. I want to get GERP scores for each position.
From what I've read, Annovar gets GERP scores for coding regions only, but I included the -otherinfo option as mentioned here: http://annovar.openbioinformatics.org/en/latest/user-guide/filter/#gerp-annotations.
Should I replace the Annovar annotation with scores or elements for the whole genome? If so, which file do I have to replace? My guess is hg19_ljb26_all.txt.
Should I replace it with hg19 elements, or base-wise scores? They are located here: http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html