These are chat archives for dereneaton/ipyrad

4th
Feb 2018
Isaac Overcast
@isaacovercast
Feb 04 2018 18:56
@cwessinger Actually yeah there's a really easy way to find this. If you look in the stats file in the output directory you'll see something like this:
## The distribution of SNPs (var and pis) across loci.
## var = all variable sites (pis + autapomorphies)
## pis = parsimony informative site (minor allele in >1 sample)
## ipyrad API location: [assembly].stats_dfs.s7_snps

      var  sum_var    pis  sum_pis
0   36589        0  75964        0
Isaac Overcast
@isaacovercast
Feb 04 2018 20:11
The number of loci with 0 variable sites is what I think you're looking for (monomorphics). Is that right?
cwessinger
@cwessinger
Feb 04 2018 20:12
@isaacovercast That's great. Thanks!