UnifiedGenotyper - pooled data - multiple samples - ploidy of one pooled sample or all?

mrood

Thank you for developing a great set of tools and adding in the ploidy option to the UnifiedGenotyper! My question is in regards to the ploidy argument when calling multiple pooled samples together. If I have pooled samples from the same population at different time points and want to call SNPs with multiple sample awareness, do I use the ploidy of one sample or that of all samples. For example, if I have pooled samples of approximately 25 haploid genomes each from three different time points from the same population should I use 25 or 75 as my ploidy?

Geraldine_VdAuwera

If you have 3 distinct BAMs with different SM tags you can use 25 and get multi-sample calls.

mrood

Thank you!