Hi! This is my situation. I recieved a file in impute2 version and I need to do a mendelian randomization analysis. My plan was:
1. Convert the file to a plink format 2. Import those files in R 3. Do the GWAS analysis 4. Select de SNP's associated with a specific trait 5. Import data to Stata, build the genetic score and do the MR analysis
This make sense to you?
I downloaded Plink 1.07 and it runs in my personal computer but when it starts this comes up:
Web-based version check ( --noweb to skip ) Recent cached web-check found...Problem connecting to web Writing this text to log file [ plink.log ] Analysis started: Wed Feb 14 17:36:17 2018 Options in effect: Before frequency and genotyping pruning, there are 0 SNPs 0 founders and 0 non-founders found 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 0 SNPs ERROR: Stopping as there are no SNPs left for analysis
And I cant run any command because it says: it is not recognized as an internal or external command
What can I do?