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.

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  • cpsosa0006cpsosa0006 RochesterMember

    Thanks Sheila. I'll look at this carefully.

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