Hi-
We are trying to relate some of the Illumina imputed genotypes to other ROSMAP traits, but the dosage files (which appear to be in *.gen format) do not have a .sample file associated with them. In contrast, for the Affymetrix data there is a .csv file with IDs. Can you please advise where we can find the IDs for the Illumina imputed genotypes? Or does the .fam file for the raw Illumina data map directly to the imputed data?
Thanks,
Corey
Created by Corey McMillan mcmillanc Thanks for clarifying!! @sieberts Thanks for this! I added a link to that fam file in the Methods description wiki for the SNP Array folder so that it's surfaced on the portal. Corey-
The CHOP samples are ordered according to the 'raw' input files: https://www.synapse.org/#!Synapse:syn7769936.
@amap it may be a good idea to put a link to this file in the directory storing the imputations, as we get this question occasionally.