Question

Question Posted 12/01/16:
For the VCF SNPs file, how do we genotype the participants. I found in an online guide that the '11AD40929_POLY' column gives you a key. They stated that 0/0 represents homozygous reference allele, 0/1 represents heterozygous for ref/alt allele, 1/1 represents homozygous alt allele. Is this correct? If not can you provide a guide? Also, in my file column for the SNPs of interest I do not have code 0/0, there is only 0/1, 1/0, 1/1 or 1/2 in the columns.

Please help me by providing instructions on how to genotype from the VCF file or turn me to a resource that I can read for answers.

Thank you!
Response posted 12/01/16 by Kwangsik Nho:
In the LONI, there are two data sets for VCF files generated from the ADNI WGS project. Please use the VCF files generated by the BROAD Institute. The genotype notation in the VCF files is that 0/0 represents homozygous reference allele, 0/1 represents heterozygous for ref/alt allele, 1/1 represents homozygous alt allele. "I do not have code 0/0, there is only 0/1, 1/0, 1/1 or 1/2 in the columns" means that the SNP has no homozygous reference allele.
Response posted 12/02/16 by Jenna Blujus:
How would a 1/2 code be genotyped?
Response posted 12/03/16 by Kwangsik Nho:
There are multiallelic sites in the VCF.