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  • Identifying species specific sequence differences

    Hi,

    I have recently assembled exon-capture next-generation sequence data from two closely related species of deer against the cow genome. I assembled the next-gen sequences using Geneious, and output the results as a series of BAM files (one file for species and each cow chromosome, 60 file in total).

    Geneious was really useful in identifying SNPs within exons within species. However, I now need to identify SNPs between the two species. There are far too many exon sequences to manually perform the comparisons necessary do this. Can anyone suggest a pipeline to automate this process?

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