Separating alleles in a bisulfite converted PCR product

Question

[jamesm2]

Hi Folks, This is a pretty basic question, I have a BS converted PCR product sequenced on a MiSeq which spans a heterozygous SNP. Fastq files have been converted to fasta in python. I'd like to separate the alleles based on the SNP call and then look at the methylation on each strand. Has anyone attempted this before or used a .py script they are willing to share. I'd love to hear how you did it.

best wishes,