These are chat archives for dereneaton/ipyrad

3rd
Apr 2017
Isaac Overcast
@isaacovercast
Apr 03 2017 04:16
@natagalle How did you calculate pi? If you were comparing SNPs between the loci and the vcf file did you take special note that the 0 vs 1-based indexing for these files? dereneaton/ipyrad#230
Isaac Overcast
@isaacovercast
Apr 03 2017 04:22
This has been an annoying bug for a while, so I actually just fixed it. The fix will go up to conda with the next release, so for now just be sure you're accounting for the +1 difference between .loci and .vcf when verifying snp status.
natagalle
@natagalle
Apr 03 2017 14:01
@isaacovercast Thanks!! I found out what happened. it turns out that I have many loci with with low frequency sites. When I filtered out sites with MAF>0.01, the few different sites across individuals were removed, leaving me with a bunch of monomorphic loci.
Isaac Overcast
@isaacovercast
Apr 03 2017 15:08
That makes sense. Glad you figured it out.