I think GATK is a great toolbox. There a quite a few steps involved and I was wondering on the impact and importance of joint genotyping - in particular when working with very small sample sizes (around 10 -15 samples). I read that it can lead to a loss on unique snps, which we would be particularly interested in. Has anymore experience with this and can tell me about the effects on the outcome? In particular in quantitative terms, do I gain many more overlapping SNPs - do I loose a lot of unique SNPs? Or is the impact negligible?
Thanks for your input!