augur refine, it seems
clock-filter-iqd 4 has been enough to get rid of major outliers in most analyses I have been seen. I’m using this parameter in an analysis with 3300 genomes, but
clock-filter-iqd 4 removes nearly half of the genomes shown in the clock view below.
If I remove
clock-filter-iqd, no tips are pruned, as expected. But even if I set it to
clock-filter-iqd 100, it still removes 1000+ genomes from the build.
By inspecting the tree above on TempEst, that is the root-to-tip plot and distribution of residuals I get.
I’m trying to only get rid of the samples on blue above (n ~ 40), but I have neither figured out how to set
clock-filter-iqd to do so, nor why
augur refine is purging 1000+ samples, no matter how
clock-filter-iqd is set up.
Does anyone know what may be wrong?