approaches for discovering proximal snps?

[cpendlebury]

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!