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auton1
Setting a proper theta in filtered/subsampled SNP datasets
Dear Adam,
After reading the manual it sounded like a minor mis-specification of theta doesn't affect the estimate of rho that much. But I hope to understand the proper method for setting theta if I have quality-filtered my segregating sites (e.g. based on allele frequency, SNP quality and sequencing coverage). If I use the input file format that only shows segregating sites (format 2), wouldn't that lower the estimate of theta? Should I go ahead with this lowered theta or instead estimate theta by other means and use that to generate a look-up table?
Another related question: do the pre-generated lookup tables in lk_files/ work for genotype datasets?
Best Regards, Ray
Depending on your exact situation, one suggestion would be to estimate recombination results using a range of (reasonable) theta estimates. My expectation is that the results should be qualitatively similar.
Yes - the likelihood files should work with genotype data, although it often better to provide phased data if possible.
On 9 October 2017 at 02:57, Ray [email protected] wrote:
Dear Adam,
After reading the manual it sounded like a minor mis-specification of theta doesn't affect the estimate of rho that much. But I hope to understand the proper method for setting theta if I have quality-filtered my segregating sites (e.g. based on allele frequency, SNP quality and sequencing coverage). If I use the input file format that only shows segregating sites (format 2), wouldn't that lower the estimate of theta? Should I go ahead with this lowered theta or instead estimate theta by other means and use that to generate a look-up table?
Another related question: do the pre-generated lookup tables in lk_files/ work for genotype datasets?
Best Regards, Ray
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Hi Adam, thank you for your help. I will try with different thetas. We only have ~60 individuals for our fish, which may be too low for phasing with accuracy.