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Unified Genoptyper joint calling on poolseq data: variable ploidy
I know Unified Genotyper has been superseded by Haplotype Caller, though due to time constraints (and other) I am committed to use UG. I have 14 population pools with variable numbers of individuals in each (16-38 genomes; ave 23) to use in my joint SNP call. I have included the BAMs as a .list in the command line but under -ploidy I have used the average number of genomes (i.e. 23).
What does -ploidy actually do in UG? If it is significant in my specific circumstance, can I include each pool's genome number using joint calling? Can I correct any bias during the filtration step following the SNP call?