Hi, I have used XHMM to identify CNVs from our exomes. But for many cases the high score deletions/duplication called by XHMM are not getting correlated with visualization of bam through IGV. If a region is called as deletion in only one individual by XHMM and when we visualize the region through IGV, the region has same coverage when compared to other exomes. Can anyone explain me why this is happening and how can i rectify this?
Hard to tell from here what's going on... For one of the problematic regions, can you post a screenshot of IGV and associated records from XHMM? One possibility is that the BAM profiles you are looking at are not normalized for library size. Also, for large regions, like CNVs, it's better to convert BAM to bigwig or tdf format for visualization.