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HaplotypeCaller - ploidy for pooled samples of bacterial genomes

anid_genomesanid_genomes University of OttawaMember

Hello,

I have an experiment where I've sequenced pools of individuals from bacterial populations. Based on the guidelines for setting ploidy, I think I should set this to the average read depth because I don't know how many individuals are in each sample (but the number of individuals greatly exceeds the read depth). Does this make sense? If so, should I set the ploidy individually for each library (I have 96 in total), or is it okay to take the average depth across all libraries as an approximation and use the same value for all libraries.

Thanks!

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