These are chat archives for dereneaton/ipyrad

26th
Jan 2018
tim-oconnor
@tim-oconnor
Jan 26 2018 15:40
Hi Deren and Isaac. I have ddRAD data from a species with multiple ploidy levels (diploid, autotetraploid, autohexaploid). Ultimately I want a dataset with loci clustered across all samples irrespective of ploidy. I have two questions. First, does ipyrad only store two alleles per locus per individual regardless of "max_alleles" value (this was the case in pyrad)? Second, is there a way to apply a different max_alleles_consens value to different samples? If not, my plan was to run ipyrad on each ploidy level separately and then cluster the loci across ploidy levels with vclust. I'm open to other suggestions! Thanks for any help.
tim-oconnor
@tim-oconnor
Jan 26 2018 18:13
Never mind -- I see that the solution is to merge the assemblies within ipyrad. Sorry fo the spam!