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stevemussmann / BayesAss3-SNPs

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
GNU General Public License v3.0
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Does BA3-SNPs require bi-allelic loci? #13

Closed jzhan6 closed 1 year ago

jzhan6 commented 1 year ago

I am new to the BA3 and I feel the inputs for this software should be all bi-allelic loci. Am I correct?

stevemussmann commented 1 year ago

It can handle >2 alleles per locus.

jzhan6 commented 1 year ago

Thanks for prompt reply. So all loci for BA3 should have more than 2 alleles and loci with only one allele should be removed from input for BA3?

stevemussmann commented 1 year ago

I would recommend removing any loci with a single allele since they will not be informative and will only increase computation time and memory usage.

jzhan6 commented 1 year ago

Thanks for your reply. I ran the BA3-SNPs, but I am a bit confused with the results. We want to calculate the migration rates between samples from several localities of the same species. All migrations are around 0.01, eg: 0.012, 0.008 and even for samples at the nearly same locality although different years, their migration rate is around 0.01 not higher than that between samples at far away localities. The results make me extremely confused. For most locality, we have 3 samples but we can around 5000 SNPs although data for samples samples are missing in some loci. Does this happen due to small sample size?

stevemussmann commented 1 year ago

This paper has some information that might be useful to you. There are a lot of properties of a dataset that can influence BayesAss results:

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2007.03218.x