I have a set of eight Illumina-sequenced trios for an organism, for which a reference genome is available. I'd now like to call genotypes on these data taking advantage of both a "classic" multisample and trio-aware approaches. I understand that bcftools (part of samtools suite) can do trio-aware calling, but I'm not sure it can work with multiple trios. At the same time, GATK (and samtools too?) can run a Bayesian model based on observed allele frequencies assuming a flat population structure.
So my question is - are there any tools that can combine both approaches?
Thanks a lot!