Question

Question Posted 10/14/14:
I just downloaded the PLINK-format version of the variant calls derived from the ADNI WGS data.
Having a quick look at the .bim file, I notice that location data is missing ("0" value in chromosome, genetic distance and base-pair position columns)
Could you please tell me if this could be fixed ?

Also, I notice that for many variants, including some identified by rs-IDs, the name of one of the alleles is missing ("0" value instead of A/T/G/C)...
Could you please explain me what it means, if it isn't a bug ?

Many thanks in advance,
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Jérôme
Response posted 10/14/14 by Sungeun Kim:
First of all, PLINK file is NOT variant call from the ADNI WGS data. It is genotype data using Illumina Omni2.5M concurrently collected with the ADNI WGS.
In order to generate files, we used Illumina manifest (HumanOmni2-5_8v_A.bpm). I suggest you to directly contact the Illumina Technical Support to get the exact answers to your remaining questions.