Open AleSR13 opened 2 years ago
Hello @AleSR13! I also just encountered a sample that was determined to have the O-9, 46 allele and the serotype Ouakam and was also flagged for contamination. The three alleles detected are completely identical to what you shared above.
Is this result a bug? I'm curious if you ever identified evidence of contamination in your sample?
Hi @michellescribner ! Sorry for the late reply. I never got to hear from them and sadly I changed jobs (and even field) so I don't know what was the solution. Sorry that I cannot be of more help.
Hello! First, thanks for making this very nice package. We use it a lot in our insititute. I wanted to report what I think is a small bug. We had a sample that was determined to have the O-9, 46 allele and the serotype Ouakam. However, we got a note on it saying:
If I look at the extracted alleles, I see that three alleles were found:
I was reading about it and it has been reported that the only difference between O-antigen 09 and 09,46 is this wbaV allele. Looking at your code, it indeed seems that if a sample has the ) O-9,46_wzy allele + the O-9,46_wbaV, you do not consider it as 'contamination' but just as a normal O-9,46 allele. However, I think that you do not do the same if the wzy is found only as a partial allele and therefore, in my example, it is marked as a contaminated sample. I have not tested whether this is the issue but I assumed that by reading your code. I am also assuming that this is not deliberate but it could be that you have a good reason why you don't give the same treatment to the partial allele. If you need more information or you prefer me to change the code myself and do a pull request, I am happy to do it.
Some info: Using SeqSero2 v1.1.1 through a conda environment. This yaml file was used to make the environment: