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  • approaches for discovering proximal snps?

    Hi all, I was wondering if you could please recommend an approach for calling and annotating proximal snps in a non-human sequence, given:

    - Agilent microarray data from 6 animals,
    - 700 SNPs to call
    - ~2x low coverage genome reference

    For each SNP I need to find in 400bp which base is the SNP, and whether there is another proximal SNP within that 400bp.

    Are there existing Bioconductor tools for this or will I need to write my own?

    Thanks!

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