I trying to detect variants in a population of haploid genomes with UnifiedGenotyper, using the -sample_ploidy option to specify the number of haploid genomes in the pool. I would like to be able to specify other options, but so far the ones I have tried do not seem to work. I have tried: -out_mode EMIT_ALL_SITES --sample_ploidy 50 -minIndelFrac 0.05 --genotype_likelihoods_model BOTH -pnrm EXACT_GENERAL_PLOIDY. Could you please tell me which, if any, of the other commands are available when calling variants on non-diploid samples? Specifically, I would really like to be able to call indels too.
Thanks for your time and help.