Verify BS-SNPer output makes sense

[yaaminiv]

GOALS: Verify that 1) loci identified by BS-SNPer are indeed SNPs and 2) those SNPs do in fact overlap with DML identified by methylKit

I used BS-SNPer to identify SNPs in my Manchester data in this Jupyter notebook:

• example BAM file from one sample
• example SNP output from one sample
• example of C/T SNP output filtered from file above

I then created a list of all unique C/T SNPs generated from each individual sample and merged BAM file (found here), then looked at overlaps between C/T SNPs and DML (DML list found here) in this notebook.

Can someone go through these example files and confirm that I indeed identified SNPs? The major question we discussed at science hour is that if methylKit is calling DML where there is data for all samples at a CG site, then why are 20% of these DML overlapping with C/T SNPs? Wouldn't a C/T SNP indicate that there is no cytosine at that position? @mgavery do you have any insight?