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3.1 years ago
timothy.delory
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20
I am using LDHat (interval option) to get rho estimates with a VCF, and I have been getting really high rho values (eg > 200) between loci. When I convert to the rho values to centiMorgans, the genome wide rate cM/Mb is not biologically feasible (eg > 1000 cM/Mb). For those you who get recombination rates through LDHat or similar approaches, have you encountered these artificially high rho values before? If so, what was the culprit? I am not getting any errors. For the record, I split my scaffolds into small segments of SNPs, so I don't think it's a convergence problem with the MCMC. Any help or resources are greatly appreciated!
