Question: Compare positions of GWAS SNPs to peaks called in MACs
gravatar for cmharro
2.7 years ago by
cmharro0 wrote:


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?

snp position catalog gwas macs • 919 views
ADD COMMENTlink written 2.7 years ago by cmharro0

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

ADD REPLYlink written 2.7 years ago by venu6.4k

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

ADD REPLYlink written 2.7 years ago by YaGalbi1.5k
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