These are chat archives for dereneaton/ipyrad

8th
Dec 2016
MINQICAI
@MINQICAI
Dec 08 2016 09:04
Hi @isaacovercast I think i met the same promble with @amelymartins. When it run to S7, always got an error"vcf build chunk 242190, Memory error",then rerun from S7 always the same even after i change to the latest version and didn't require vcf outfmt. Now I'm doubt that if any promble when i change to latest version ipyrad. Beause I just replace the ipyrad file download form "dereneaton/ipyrad" without any command. As you mentioned "conda install -c ipyrad iprad". many thinks for your contribution!
joqb
@joqb
Dec 08 2016 16:04
@dereneaton Sorry to ask again but why did the .allele file disappeared? That was pretty nice to work with polyploids. Any particular reason why it was omitted in ipyrad? Any hope to see it coming back?
Deren Eaton
@dereneaton
Dec 08 2016 16:46
@SnakeEvolution_twitter Glad we fixed one problem. Damn about the VCF error. I'll look into it. Thanks.
Deren Eaton
@dereneaton
Dec 08 2016 16:52
Hey @joqb, I'm hoping to provide something similar eventually, the problem with the pyrad alleles file is that the alleles are only phased correctly when we enforce that reads must align almost completely, i.e., they are not staggered in their overlap. So the alleles are correct for RAD data, because the reads match up perfectly on their left side, however, staggered overlaps are common in other data sets that use very common cutters, like ezRAD and some GBS, and especially so when R1 and R2 reads merge. So we needed to change to an alternative way of coding the alleles so that we can store both phased and unphased alleles, and its just taking a while to do. So for now we are only providing unphased alleles, although we do save the estimated number of alleles for each locus. This information is kind of hidden under the hood at the moment though.
joqb
@joqb
Dec 08 2016 18:15
@dereneaton Good to know that it's not completely forgotten but just complicated.