I have access to both the imputed and unimputed genotyped SNPs of the AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6 study. For my work, I would require the data in **Plink format ( .bed, .bim, .fam )**. What can be the way to convert the imputed dosage files into Plink format? I have tried looking for commands on the internet but found no resources for converting **.chop.dosage** files to **Plink** format. Any help will be much appreciated.
Created by Md Shamsuzzoha Bayzid Bayzid Hello!
I am not sure if these dosage files _can_ be converted to .bed, .bim, and .fam files since they seem to have slightly different information. There is a .fam file that corresponds to the imputed data here: syn5879839 but I'm not sure that dosage values can be directly converted to .bed/.bim.
I found this old thread, which has some discussion on using PLINK with these dosage files: https://www.synapse.org/#!Synapse:syn2580853/discussion/threadId=2511, which also links to this page: https://zzz.bwh.harvard.edu/plink/dosage.shtml
I'm not sure if this is helpful or not.
Otherwise, you may need to contact the authors for clarification on whether these can be converted.
Let me know if you have any other questions,
Jaclyn
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AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6 Imputed Data converting to Plink Format page is loading…