Compare positions of GWAS SNPs to peaks called in MACs

Question

[cmharro]

Hello,

I have downloaded a list of SNPs from the GWAS Catalog, and I want to compare the positions of these SNPs to see if they overlap with peaks called in MACs from sequencing data. What is the best way for somebody with limited bioinformatics experience of doing this?

[venu]

You can use intersectBed feature from bedtools. Prepare your SNP file in bed format and follow this

[BioinfGuru]

venu - I want to do this also, but map human GWAS to mouse peaks....suggestions?