My VQSR tranches-plot shows cumulative variants in tranch 0-90, 90-99, 99-99.9

Martin_ZieglerMartin_Ziegler Member
edited August 2017 in Ask the GATK team

Dear GATK-Team,

My VQSR tranches-plot (exome data) shows cumulative variants in tranch 0-90, 90-99, 99-99.9. To my understanding it should be the other way round (like in your article link).

My tranch file is:

# Variant quality score tranches file
# Version number 5
targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity
90.00,1047316,37823,2.1789,1.2078,3.4763,VQSRTrancheSNP0.00to90.00,SNP,664834,598350,0.9000
99.00,1256170,54507,2.1551,1.2197,0.1249,VQSRTrancheSNP90.00to99.00,SNP,664834,658185,0.9900
99.90,1303686,68389,2.1437,1.2255,-4.2698,VQSRTrancheSNP99.00to99.90,SNP,664834,664169,0.9990
100.00,1338832,87080,2.1302,1.2417,-1299.3394,VQSRTrancheSNP99.90to100.00,SNP,664834,664834,1.0000

Greetings

Martin

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