Making random SNP with similar allele frequency and recombination rate to my SNP list

Question

[seta]

Hi all,

For some tests, I would like to generate about 2000 random SNPs. As I found in some papers, the random SNP should have similar allele frequency and recombination rate to my SNP list. I have allele frequency of my SNP list, but no information about their recombination rate. Could you please help me out how I can generate such the random SNP list, 1000 times?

Thanks in advance

[Fabio Marroni]

Depending on the data you have, you might try simcoal2 or genomepop.