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Question Posted 12/04/18:
I am new to the genetic data introduced by ADNI. I wanted to know how to extract the most-related SNPs to AD.
Thanks in advance
Response posted 12/05/18 by Kwangsik Nho:
First download all plink files from ADNI and then extract the SNPs from the plink files using PLINK software.
Response posted 12/05/18 by Ahmed:
Thanks so much for your prompt reply.

I have downloaded the file "ADNI GO/2 SNP genotype data - Complete PLINK for sets 1 - 9". I used PLINK to analyze the data and did basic steps as filtering and Hardy-Weinberg Equilibrium. My question are as below:
1) Is the above file the correct one i should use (after reading in plink it says total of 432 people (236 males, 196 females) loaded from .fam.).
2) Can you please provide me the main steps I need to follow to extract the SNPs or refer me to any detailed reference with these steps?

Thanks so much and sorry for inconvenience
Response posted 12/06/18 by Kwangsik Nho:
In Plink, we can use —extract option. First create a text file containing target SNPs an then use —extract file name.
Response posted 12/07/18 by Ahmed:
Please can you give more details on how to do it?
Response posted 12/07/18 by Kwangsik Nho:
Please look at the manual of PLINK software (https://www.cog-genomics.org/plink2). Or please consult with someone with a bioinformatics background in your institution. Because it consists of several steps including quality control procedures.
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