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Tranches plot completely off
Dear GATK team. First of all, thanks a lot for your continuous support and collaboration.
I just finished the joint genotyping of a set of ~3000 samples and got very disappointed when I took a look to the tranches plot, which is showing a vast majority of false positives in all tranches. Do you know where this may be coming from? Please find attached the SNP and INDELS plot as well as the mentioned tranches plot.