Question

Question Posted 01/25/16:
To whom it may concern,

I have questions regarding ADNI genetic data. Can you help to answer them?
1.
How many samples were genotyped using Omni 2.5?
I downloaded the OMNI file from https://ida.loni.usc.edu/
812 samples were listed in the WGS_Omni25_BIN_wo_ConsentsIssues.fam file. I know that ADNI has over 1,500 samples. Did you genotype more samples than these 812?

2.
How many samples went through whole genome sequencing?
According to your document "Overview of Variant Calling Workflow and Quality Metrics Obtained for New VCF Files on Whole Genome Sequences of ADNI Participants", 818 ADNI samples went through whole genome sequencing. Did you sequence more samples afterward?

3.
I am not familiar with the vcf files for whole genome sequencing result on the loni website. Do you have the SNP information saved in PLINK format?


Best,
Kaida
Response posted 02/01/16 by Sungeun Kim:
1. Only samples included in the WGS were genotyped by using Omni2.5M. Rest of ADNI samples were genotyped by using Human610Quad (ADNI-1) or OmniExpress (ADNI-GO/2).
2. We did not sequence more samples.
3. Please look at "vcftools" that can convert VCF to plink format.