I am looking at a few illumina WES experiments on the same cell line, trying to find a cnkit segment or bin hit on a gene that has reads and is captured in the library. I am not finding any values in all but one sample (no neutral calls, just omitted). The location is represented in the target file.
Variants were detected in this gene using GATK, the reads aren't low quality and it looks like there are enough reads to make a call in CNVkit (when I compare to neutral calls in other samples for this gene).
Does this happen because there aren't enough reads in or around the gene to make an inference in this particular sequencing run, or perhaps it was too noisy to make a conclusion? Thought I'd ask someone who may have a better grasp of the code than I do.
Thanks in advance.