VCF files from ADNI whole genomes that have been re-aligned and re-called to create new VCF files using Broad best practices (BWA and GATK-haplotype caller) in Summer, 2014 are now available from the Download -> Genetic Data section of the ADNI repository.

The new datasets are named ADNI WGS Data – GATK SNV+Indel call chr# of 23.  For technical questions about the production of the VCF files, please contact Sheila Sutti at ssutti@genetics.med.harvard.edu.

To differentiate between the CASAVA call data and the GATK call data, the CASAVA data sets have been renamed from ADNI WGS SNP Set ## of 29 to ADNI WGS Data – CASAVA SNV call Set ## of 29.