GATK supporting reads versus IGV display
Dear Staff Member(s),
I hope you can help me clarify a discrepancy between GATK & IGV. The number of supporting reads that I see reported under sampleB.AltSupportingReads(AD) for a deletion is 5. However, when I visualize the BAM/BAI files and check the exact same location I see only two reads supporting the deletion. I hope that I am providing enough information. Otherwise I can send additional information. Am I overlooking any data that would explain the difference between what GATK and my visual inspection using IGV?
Thanks for your help.