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  • SNP calling from RRBS data

    Hello,

    I am interested in calling SNPs from reduced-representation bisulfite sequencing (RRBS) read data. The purpose of this analysis is to generate a FST value among study groups to quantify divergence in the genome in comparison to that of the methylome.

    I am aware of certain programs that can identify SNPs within RRBS data such as BS-SNPer and Bis-SNP but I was wondering if anyone had any advice about which program would be most effective at doing this?

    Once SNPs have been identified, what programs would be most suitable for the next stages of the analysis, for instance visualizing the SNPs and creating a SNP panel for measuring genetic differentiation. Would GATC be suitable for this purpose?

    Finally, if there were genomic reads (i.e. not bisulfite converted) available from the same populations but different individuals, how could this data be best used to verify the RRBS derived SNPs, given some of the biases involved in generating this data?

    Thanks in advance for any advice you can give,

    Alan

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