I have WES data for a sample having a specific phenotype. I ran EXCAVATOR on that sample, trying to detect CNVs. I am interested to check deletions happening on gene A, because patients having that specific phenotype would frequently get deletions in that gene A.
In EXCAVATOR's results file: FastCallResults_Sample, I found one big deletion covering all of gene A.
When I cheked this sample on IGV, I saw that the exons of gene A are well covered, with a minimum coverage of 30 reads and reaching up to 100 reads.
My question is, is this contradicting? or did I misunderstand EXCAVATOR's results ? is there an explanation for this scenario?