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
