Genotype import error checks in progeny

I have gotten some questions recently about problems people are having with genotype imports and thought this would be a good time to send a reminder out about some of the basics of genotype importing into progeny since there are a lot of new people and the details don’t always get passed on or are forgotten.

Anyone can come to me with additional questions, but the thing I wanted to remind everyone about is performing error checks.  When you select to check for mendelian errors, or discrepancies you should check the corresponding tab for those types of errors at the end of the import to see if you have any errors and to resolve them if possible.  (See screen shot below)

You should always check for:

1) Rejected genotypes:  This will tell you if some of your genotypes were not entered.  (examples of possible reasons include a typo in the sample or marker name or your marker is not in the set you selected to import into)

2) Discrepancies:  If someone else has already typed the marker you are typing or if you re-run a plate or re-process a plate and re-import, there may be differences in what was in progeny and what you are trying to put in.  When you select to check for discrepancies Progeny will keep the original data unless you resolve the discrepancy. I am telling you this because someone recently incorrectly processed plates and imported, then re-processed and re-imported, but was still getting the original (wrong) genotypes out for analysis.  The reason was that the original genotypes were still in the database and the new (discrepant) genotypes were being held, waiting for confirmation of whether or not they should overwrite the existing genotypes. In order to overwrite existing genotypes, you must either a) resolve discrepancies, or b) not select to check for discrepancies (new genotypes will automatically overwrite what is in progeny).

Here is an example of the genotype import page.  Notice the tabs across the bottom with the different types of error checks that you should review. The Progeny user manual also has more in depth information about this.  Feel free to ask me any questions about this.

Jamie