We have replied to Yann off list, but for the benefit of others on the list who are interested in the HCP genetic data:
If you have questions about the HCP dbGaP data, please send them to [email protected]<mailto:[email protected]> – it’s a central collection place from where the questions are forwarded to the appropriate curator. With our focus on the neuroimaging and behavioral data we distribute, we no longer have a team of geneticists consulting for the HCP, so you will get your best info from the dbGaP folks who are experts in using the genetic data they distribute. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387<tel:314-362-9387> [email protected]<mailto:[email protected]> www.humanconnectome.org<http://www.humanconnectome.org/> ________________________________ From: [email protected] <[email protected]> on behalf of LE GUEN Yann <[email protected]> Sent: Tuesday, August 14, 2018 2:52:42 PM To: [email protected] Subject: [HCP-Users] Documentation HCP genetic data Dear HCP users, I am looking for the documentation of the HCP data online (other than the few pdfs and .txt in the downloaded data) ? In particular, I would like to know a few things: 1) In which version genome build coordinates (GRCh37 or GRCh38) are the HCP genetic data released? 2) Is there any correspondence files for the SNPs names on the MEGA and Neuro chips ? For example, (lines below do not provide confidential information on the subjects) the .bim starts this way: 1 1:49554-G-A 0 49554 G A 1 JHU_1.55325 0 55326 T C 1 JHU_1.56018 0 56019 C T 1 JHU_1.61461 0 61462 A T 1 JHU_1.66161 0 66162 0 A 1 JHU_1.84138 0 84139 0 A 1 JHU_1.86330 0 86331 G A 1 JHU_1.88337 0 88338 A G 1 rs376723915 0 91516 0 A 1 JHU_1.91535 0 91536 G T I would like to convert JHU_* and CHR:POS-A1-A2 in rs ids names more commonly used such as rs376723915. 3) Maybe, I haven't looked carefully for it yet.. But, do you know where is the documentation describing the content of the genetic files such as ganon*_CHR.csv, infoCHR.csv, ganong*_CHR.sas7dbat, infoCHR.sas7dbat, fin_hcp_dose_cCHR_chunk*, hcp_impute2_chrCHRchunk*, etc .. ? and recommended protocol to read/convert them for further analysis? These are text files likely readable as dataframes and their content is partly described by their columns names. However, I am looking for a documentation that would already gather all information and an efficient way to convert them to plink or bgen format (smaller binary files). Best regards, Yann _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
