I ask you help because I'm in a situation I struggle with. I am working o a project with the aim to find somatic mutation in a certain tumor. To achieve this whole exome seq. was performed on paired tomor-blood samples. I got into the project after the actual sequencing was performed and my duty was to analyse the data. After a while I was still working on them because despite the apparent good quality of the experiment something seemed wrong in the mutations I called.
Asking questions to the lab's boss I find out that the WES was not run with pairing blood-tumor samples, but rather They did 2 different runs: one with all the bloods from all the patients and one with all the tumor DNA samples.
I guess the intrinsic bias of the machine is relevant in this case and I really do not know for sure how to handle it. I guess many of the somatic mutations I called did not pass the validation test (q-PCR and ddPCR) for this reason.
Does anyone have some tips on how to "clean" the data? Thank you so much