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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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I know Unified Genotyper has been superseded by Haplotype Caller, though due to time constraints (and other) I am committed to use UG.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?