Consensus on how to select SNPs for creating a phylogeny when the full dataset is too large I have got a quite large VCF file (about 20k samples with 160k SNPs after filtering for quality etc.) and I would like to get a phylogeny for it. However, the whole dataset's too large for my computational resources (unless I go for fasttree which would be my last resort). Therefore, I need to subset the SNPs and there's plenty of possible ways to do this (dump all rare SNPs with MAF below a threshold, only use SNPs in coding regions, only use missense SNPs; just to name a few).
Is there a consensus (or at least some comparative work or recent review; I found nothing) on what method works best and gives the tree that's closest to using the full dataset?
The subset that gives you the tree closest to the one you obtain with the full dataset does not necessarily is the tree nearest to reality... It could be that you get a more realistic result using only partial data for multiple reasons. Your best chance is in my opinion, as it usually is, making lots of tests and contrasting hypotheses.