Open qsonehara opened 11 months ago
First note that if the heterozygous SNP creates a CpG that isn't present in the reference, then you'll only see output for that site when --modsites-mode
is set to the denovo
option.
When output is generated for a heterozygous SNP site, I believe the current logic will give the non-CpG reads a methylation probability of zero, and count them towards the unmodified coverage.
Thanks for your reply!
To my understanding, if one has a heterozygous SNP on a fully methylated CpG site, the modification probability will be evaluated as ~0.5. Such a site needs attention in interpretation, especially when the interest is in the effects of epigenetic regulation. I think it could be helpful if the counts of non-CpG reads were shown for each site in the output.
Thanks @qsonehara , I think this is a good suggestion for us to have as an option, we can leave this as an feature ticket and see if it can be added in a future update.
Hi,
I'm wondering how the genetic variants on CpG sites are treated by aligned_bam_to_cpg_scores. For example, when a diploid genome has a heterozygous SNP on a CpG site, how will the coverage and modified/unmodified site counts in output files be affected?
Best, Kyuto