Extracting SNP annotations

If you have genotype data available on the same individuals with methylation profiles you can check for ID mismatches. The methylation arrays have 65 SNPs which can be extracted from the methylation data. These 65 SNPs can be compared to genotypes measured with genotype arrays. You can find more information on how to do this in Sample QC.

You can find a list of snp names here: https://github.com/perishky/meffil/blob/master/docs/snp-names.txt