Hello all,
I am analyzing a cohort of 10 patients for SVs. Approximately half of the patients report no INSs, while the others do. I am seeing what appears to be a normal (the standard seen in the other patients) number of calls for all the other SVs.
Trying to troubleshoot this issue, as the number of INSs should be higher than the other calls based on the results that showed INSs, and having zero in some of the patients calls my whole pipeline into question. Could it be an issue with my aligner? Doesn't appear to be related to sequence quality, as most of my data is fairly similar and there is no division between those that have INS and those that don't.
Is there is a parameter that I could change to increase sensitivity to INSs.
If anyone has an idea what could be going on, please let me know
I am analyzing a cohort of 10 patients for SVs. Approximately half of the patients report no INSs, while the others do. I am seeing what appears to be a normal (the standard seen in the other patients) number of calls for all the other SVs.
Trying to troubleshoot this issue, as the number of INSs should be higher than the other calls based on the results that showed INSs, and having zero in some of the patients calls my whole pipeline into question. Could it be an issue with my aligner? Doesn't appear to be related to sequence quality, as most of my data is fairly similar and there is no division between those that have INS and those that don't.
Is there is a parameter that I could change to increase sensitivity to INSs.
If anyone has an idea what could be going on, please let me know