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Count of False Positives
After applying VariantRecalibrator, I am examining the SNP.tranches.pdf and SNP.tranches table output files. I am wondering, is it possible to get a count of the tranche-specific false-positives? This value isn't immediately obvious to me in the SNP.tranches table but is plotted in the graph in SNP.tranches.pdf and I would like to access those values.
My SNP.tranches table is shown here:
# Variant quality score tranches file # Version number 5 targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity 80.00,420195,76067,2.4862,2.0882,3.8931,VQSRTrancheSNP0.00to80.00,SNP,525369,420295,0.8000 90.00,472716,100489,2.4582,1.9875,2.2868,VQSRTrancheSNP80.00to90.00,SNP,525369,472832,0.9000 95.00,498977,113066,2.4434,1.9268,1.0517,VQSRTrancheSNP90.00to95.00,SNP,525369,499100,0.9500 99.00,519990,124866,2.4257,1.8821,-0.5150,VQSRTrancheSNP95.00to99.00,SNP,525369,520115,0.9900 99.90,524717,144668,2.4167,1.7196,-3.2399,VQSRTrancheSNP99.00to99.90,SNP,525369,524843,0.9990 100.00,525243,147612,2.4118,1.6796,-73.9905,VQSRTrancheSNP99.90to100.00,SNP,525369,525369,1.0000
Thanks so much. (And this is whole-exome data and I am following the Best Practices Guidelines - although we are using GATK version 3.5, this is a choice we made for the purpose of ensuring the highest possible consistency with older data called using version 3.5)