subset bead chip (ovine 50K illumina)

Question

[landivincenzo]

Hello, I want to work with beadchip SNPs data (50,000 SNPs from ovine illumina beadchip). I want to extract from a set of SNPs/population a subset of 100SNPs filtered by polymorphism and searching by omogeneus chromosome distribution (2-3 for chromosome) to use for parentage testing. there are some R script or any tools I can use?

Thank you very much for any help