What does the warning: "Bad alleles for marker '', expecting 'a/c' found 'a/g' mean?

[ghost]

Hi, I am getting a lot of warnings with the above text.

I found the source code origin of the warning:

 if (allele1[marker] == "")
                allele1[marker] = tokens[firstColumn],
                allele2[marker] = tokens[secondColumn],
                original_flipped[marker] = flip ? 'Y' : 'N';
            else if (tokens[firstColumn] != allele1[marker] ||
                     tokens[secondColumn] != allele2[marker]) {
                if (++badAlleles > maxWarnings) continue;
                printf("## WARNING: Bad alleles for marker '%s', expecting '%s/%s' found '%s/%s'\n",
                       (const char *) tokens[markerColumn],
                       (const char *) allele1[marker],
                       (const char *) allele2[marker],
                       (const char *) tokens[firstColumn],
                       (const char *) tokens[secondColumn]);

But I can't understand what comparison is being made. It happens when I process the very GWAS file, so it is not comparing alleles with the other GWAS results. It reads as if it is being compared to a reference build but I dont see that in the source code.

Any further info would be appreciated.

[cwnag-c]

I alsohad the same problem, did you solve this problem?

[dbw198211]

I met this problem too, how to solve this problem?

[Stacy33333]

Did anyone solve this problem? I also met this error.