Hello, I have been approved for access to the PsychENCODE distribution. I want to download the data listed under the Raw data->Genotypes section at http://resource.psychencode.org/. But: (1) When I follow the first link 'Merged Integrative and Cross-Disorder Genotypes controlled', an empty table results. (2) When I follow the second link 'Imputed Genotypes', I also get an empty table. (3) When I follow the third link 'Metadata for Imputed Genotypes controlled Phenotypes' the page seems to be hanging on 'Loading'... Can you assist? Thanks, Elisabetta P.S. I've tried an alternative route, that is going from https://www.synapse.org/#!Synapse:syn9947370, where there seems to be a total of ~73GB of data. Is this a superset of (1) and (2) above?

Created by Elisabetta Manduchi manduchi
Hi Mette, just following up on this again -- it would be great to be able to access at least the same genotype matrix that was used in the publications. I'm not sure it would be possible to reproduce those published *QTL analyses simply by cobbling together genotypes from the various projects, since there are many steps along the way where we might make alternative decisions about parameters, etc. that would result in a different genotype matrix. Could you please at least make that matrix available, if for no other reason than to facilitate reproducibility? Thanks!
I'd like to second this question. Thank you!
Thank you Mette, I think the OP of this thread and myself and probably others were aware that the disparate data were already available for each project, but I think what we're looking for is something that wouldn't necessitate downloading all of the various files and then merging and subsetting them to re-create what was used for the analysis. You seemed to allude to the existence (or at least need) of such a merged file in your 6/24 reply. I think that's what most folks in this thread would be interested in -- can you give an update on when that will be released?
The imputed genotypes for the Capstone data are available for each [data contributing study through this query](https://www.synapse.org/#!Synapse:syn8466658/tables/query/eyJzcWwiOiJTRUxFQ1QgKiBGUk9NIHN5bjg0NjY2NTgiLCAic2VsZWN0ZWRGYWNldHMiOlt7ImNvbmNyZXRlVHlwZSI6Im9yZy5zYWdlYmlvbmV0d29ya3MucmVwby5tb2RlbC50YWJsZS5GYWNldENvbHVtblZhbHVlc1JlcXVlc3QiLCAiY29sdW1uTmFtZSI6ImFzc2F5IiwgImZhY2V0VmFsdWVzIjpbInNucEFycmF5Il19XSwgImluY2x1ZGVFbnRpdHlFdGFnIjp0cnVlLCAiaXNDb25zaXN0ZW50Ijp0cnVlLCAib2Zmc2V0IjowLCAibGltaXQiOjI1fQ==). It does have the disadvantage that it includes all data, and not the specific samples used in the analysis available under http://resource.psychencode.org/. To help that we will post a list of the genotyping IDs specific to the analysis on the resources site. Do be aware that data from resources not available through this portal were also included, such as GTEx.
I would like to second this -- any update on the availability of merged/imputed genotype files? Thanks!
Hi Mette, just to follow up here, do you happen to know when the merged integrative genotypes will be available?
OK thank you!
There is a merged set of the imputed genotypes used for the data on the resources page (the merged integrative genotypes). It is undergoing an update. We will let you know as soon as it is back in place

Problem accessing the Genotypes data from resource.psychencode.org page is loading…