SNP enrichment test along the genome

[capricy]

Hello, there,

I have SNP annotation along the genomic DNA. By visual inspection, I can tell that some chromosomal region tends to have more SNPs than the other. I wonder if there is a tool to statistically analysis such enrichment along the genome?

For example, I can calculate the number of SNPs along each 5k genome region, and also the average number of SNPs long the whole genome (total number/length of genome), how would I find the genomic regions that have significant higher number of SNPs when compared with this average SNP number?

Thanks a lot!

C.

[yzzhang]

fisher exact test maybe fit this.