Question Posted 12/22/14:
Today (Dec 22th, 2014), the sample IDs in vcf files of ADNI WGS GATK are still in the previous format such as 08AD6536, 08AD6540, and so on.
Also, the csv file (ADNI_PTID_WGS_Sample_correspond) under adniomni does not contain information for matching these IDs to RID or PTID.

Also, the vcf file chr 9 is not the one that we expected. It links to the file "ADNI.808_indiv.minGQ_21.pass.ADNI_ID.tar." This file is empty.
Response posted 12/22/14 by Andy Saykin:
The file name problem with chr9 has been corrected. The current version should have ADNI IDs to link to other data.