Hi! I'm running ipyrad on my samples and there is something I can't understand. My first run included 8 samples, using the default parameters and all steps (1-7) I got a
total_prefiltered_loci of 61907. I wanted to see if I could get more loci reducing the number of samples to 6 (removing the most divergent and different ones), so I create a branch with a subset of samples and I ran only the steps 6-7 using the force flag (-f). I end up with less loci (total_prefiltered_loci of 44107). This patter keep happening, when I try to include only 3 samples highly similar with high sample coverage the total_prefiltered_loci is 20483 and I end up with no loci, all of are filtered in the process. Am I using the branching wrong??