Question Posted 06/28/17:
Dear ADNI,

Some VCF files for WGS data have variants with genotype calls of ./. , instead of 0/0, 0/1, or 1/1, even though these variants pass all filters. Could you please explain what this means and propose some solutions of how to treat these variants?

Thank you,
Response posted 06/28/17 by Kwangsik Nho:
There are two types of vcf files, CASAVA vcfs and GATK vcfs. Which one did you look at?