These are chat archives for dereneaton/ipyrad

Aug 2018
Aug 13 2018 11:42
Hi everyone I have my vcf. file from ipyrad and I want to extract heterozygous SNPs and read depth for each allele at that site, to assess the ploidy using R package gbs2ploidy (Gompert & Mock, 2017). If someone has already done that before, I will be grateful for his help, Thanks!
Jenny Archibald
Aug 13 2018 14:05
@isaacovercast @dereneaton - I feel this must be a stupid question, but I haven't been able to find how to get mean sequencing depth for a given accession (or even the entire dataset) from ipyrad, without using the API (which I do not currently know how to use). Can you help? I thought ave_depth_stat may be the answer, but I see that it is the same for two of my analyses that have different clustering values (.80 vs .95), which doesn't seem right. I just want an average value to report for publication. Any help is appreciated!
Eaton Lab
Aug 13 2018 16:39
Hey @andrew-hipp I've been working on rewriting step 6 to skip this long and slow databasing step (55 days yikes!). It seemed like a good idea when we originally designed it that way but now that datasets are becoming much larger it has become far too slow. The new way will be much much faster and more memory efficient and should be able to complete even super large datasets in less than a day. I hope to have it finished and available before the end of the month.
@mcfaddenlab See the ABBA-BABA link on this page:
@Siadjeu I've been interested to try this, or incorporate a similar estimator into ipyrad, but haven't had time to try it out yet.
Siadjeu Christian
Aug 13 2018 18:31
Eaton Lab thanks for your response I hope you will do it as soon as possible, it will be
great and wish you all the best for that!
Isaac Overcast
Aug 13 2018 20:04
@jenarch Yeah, this is totally available in the s3_cluster_stats.txt file in the *_clust_0.85 directory after running step 3.