Question: What causes missing GERP scores in Annovar results?
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gravatar for anp375
3.8 years ago by
anp375170
anp375170 wrote:

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

gerp annovar • 949 views
ADD COMMENTlink written 3.8 years ago by anp375170
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