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
First download all plink files from ADNI and then extract the SNPs from the plink files using PLINK software.
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
In Plink, we can use —extract option. First create a text file containing target SNPs an then use —extract file name.
Please can you give more details on how to do it?
Thanks
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.