Intersecting phyloP bed and per-base bed files

Question

[gokberk]

Hi, I'd like to intersect the phyloP bed file with a SNP-based bed file using bedtools. By "SNP-based" I simply mean a list of SNPs which looks like the following:

chr1    123 124 1
chr1    345 346 2
chr1    788 789 3

Actual chromosomal positions of these SNPs are chr1:124, chr1:346 and chr1:789, thus I formatted my bed file as "chr#, pos-1, pos".

I was following this post, and now I am a bit unsure if I formatted my bed file correctly. Because in that post a continuous bed file is converted to the per-base format as "chr#, pos, pos+1". Not that I have a continuous annotation, but don't we skip the first base and add an extra base to the end of a given continuous annotation/promoter/enhancer etc. while converting to per-base format in this way?

Any tips are appreciated, thanks!