The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.