Annotation files

[mfazel]

Hi,
As I understand, -n tells the pipeline to annotate the results
I think as the first step, it would be nice to clear up what these two files really are:
ANNO_1 = /home/mario/Documents/CCHMC_postdoc/Projects/Allele_specific_variants/SDataB_VariantsUsedForEachPhenotype.bed
ANNO_2 = /home/mario/Databases/Hsap/hg19/hg19_exons_anno.bed

a) How do I prevent annotation? Reason is, I assume -n means annotate and if I don't add it, mean's I don't want annotations. Then why it complains about not finding annotation file or I had to comment it out in the config?
b) How these annotation files should look like? Is it possible to include them in the repo or at least post the head so users know what should be the content. My guess was that a gtf to bed should work, at least for one of them.
I did not find much explanation here on github readme file about theses.