I'm analyzing GWAS data using PLINK. When I merged two datasets I got an error message "Found 167402 SNPs that do not match in terms of allele codes.
Might include strand flips, although flipped A/T and C/G SNPs will be undetected)"
I expected that issue but how people handle this? Could you advise me any protocols or papers? I'm doing case-control association study and want to know should I remove those A/T and C/G SNPs at all or there are some other ways to cope with it?
Thanks!
Might include strand flips, although flipped A/T and C/G SNPs will be undetected)"
I expected that issue but how people handle this? Could you advise me any protocols or papers? I'm doing case-control association study and want to know should I remove those A/T and C/G SNPs at all or there are some other ways to cope with it?
Thanks!