These are chat archives for dereneaton/ipyrad

Feb 2017
Bohao Fang
Feb 15 2017 14:52
Hi guys, I would like to know where is the information about SNPs position in chromesomes. Now I have my outfiles folder which contains many outputfiles and a stats.txt.
I am using iPyrad 0.5.15!
Feb 15 2017 16:06
Hi @isaacovercast, if this is of any help. I run just the reference pipeline for two of the samples for which I have a reference genome, and I am only able to recover ~ 500loci in s3, when for the denovo pipeline I recovered ~5000. I am currently running GATK to compare results, but I am wondering whether there is a mistake in the ipyrad pipeline for the reference.