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mathiesonlab / pg-gan

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NOT ENOUGH SNPs #22

Open BrinaLG opened 1 year ago

BrinaLG commented 1 year ago

Each time I run the command I get this output to the output file. Why could this issue be occurring?

saramathieson commented 1 year ago

Usually this occurs if the mutation rate is too low to consistently get enough SNPs in the given region size. There are a few ways to fix this:

  1. Increase the mutation rate
  2. Increase the average effective population size through demographic model changes (including changes to the priors)
  3. Increase the region length (L in global_vars.py)

Let me know if it works! It's not a huge problem to sometimes not have enough SNPs (since regions are padded with zeros), but since real data typically won't have this issue, you want to make sure that the simulations don't either.