I'm having the following problem with PLINK:
I am using the --freq command to calculate allele frequencies from an input that was created from 23andMe data. However all I get in the frq report is NA estimates for all minor allele frequencies:
CHR SNP A1 A2 MAF NCHROBS 1 rs12564807 0 A NA 0 1 rs3131972 A G NA 0 1 rs148828841 A C NA 0 1 rs12124819 G A NA 0 1 rs115093905 T G NA 0 1 rs11240777 A G NA 0 etc...
Same thing goes for --hwe etc. --missing is the only command that seems to be working, so I know that the file is read correctly.
I don't know what's wrong because PLINK reads the input files correctly. I suspect it is the allele coding, but I have tried several solutions and they still don't work. Has anyone come accross with a similar issue?