No error or warning for ambiguous bases
Dear GATK community and developers,
The documentation says clearly that GATK does not handle ambiguous bases. I stupidly ran GATK with a self constructed reference file and did not realise my file had ambiguous bases in it. GATK ran without errors or warnings and it was not until i looked at the called SNPs in more detail in IGB that i noticed that good SNPs were not being called because the reference was ambiguous. Although it is my own fault for not thoroughly checking my reference file, I think it would be helpful if GATK would check it before starting and and throw out a warning if it detected ambiguous bases. Perhaps other users and/or developers agree.