Methyl calling on C polymorphism present in the reads but not in the reference genome

[Marie-Joe Karam]

Hello,

I have BS-sequencing and low coverage DNA-sequencing for plant individuals. I am wondering if there's a way to do the methyl calling with bissnp by defining the C positions to look at according to the genotype of the individual itself and not that of the reference genome. I explain myself: I observed cases where my reference was T at a position, and my individual was C on that position. The methyl-calling ignored that position because it is not a C in the reference (as an example, please see the attached figure).

Thank you in advance,

Best,

Marie-Joe

[Yaping Liu]

Hi Marie-Joe,

Bis-SNP is designed specifically for the case you described. 

Are you using bissnp_easy_usage.pl? By default, it is designed for human genome. It used a lot of setting and filtering at VCFpostprocess step to filter out potential artifact in methy/SNP calling. 

From the example you showed here, there is also another 3 SNP nearby, in human genome, usually it means reads aligned falsely in that position. But plant might be different. 

If you look at the produced *.cpg.raw.sort.vcf file, it should show the site you circled in your plot. you can convert this vcf file by vcf2bed.pl tools provided.

thanks,

Yaping

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Yaping Liu, Ph.D.