I have run a GWAS with PLINK, obtaining, as output, a file with the following format:
CHR SNP A1 A2 TEST AFF UNAFF CHISQ DF P 6 6:131182784 G T ALLELIC 349/429 872/1584 22 1 2.731e-06 6 6:131179801 C G ALLELIC 349/429 874/1582 21.6 1 3.356e-06
and I would like to visualise these results using locuszoom (http://locuszoom.sph.umich.edu/locuszoom/genform.php?type=yourdata). However, I obtain the following warning/error:
WARNING: your association results file has both rsID and chr:pos SNP names. Please make sure you have selected the correct genome build by using the --build parameter, or by selecting the appropriate build on the website. Error: region specified contains no SNPs, skipping..
Even though I do not have any rsID SNP, the build parameter has been chosen correctly (actually I have tried with every build with no improvement), and there are SNPs in the specified region.
Can anyone help? Thank you very much in advance.