Question: GATK VQSR output
0
gravatar for geneart$$
6 weeks ago by
geneart$$40
United States
geneart$$40 wrote:

Hi, I performed VQSR on SNPS and then used that file to do VQSR on Indels. The tranches file ouput looks like this:

targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity
99.95,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL0.00to99.95,INDEL,8,7,0.8750
99.90,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.95to99.90,INDEL,8,7,0.8750
99.80,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.90to99.80,INDEL,8,7,0.8750
99.60,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.80to99.60,INDEL,8,7,0.8750
99.50,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.60to99.50,INDEL,8,7,0.8750
99.40,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.50to99.40,INDEL,8,7,0.8750
99.30,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.40to99.30,INDEL,8,7,0.8750
99.00,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.30to99.00,INDEL,8,7,0.8750
98.00,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL99.00to98.00,INDEL,8,7,0.8750
97.00,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL98.00to97.00,INDEL,8,7,0.8750
90.00,316,219,0.0000,0.0000,2.1470,VQSRTrancheINDEL97.00to90.00,INDEL,8,7,0.8750
100.00,390537,283098,0.0000,0.0000,-233.8228,VQSRTrancheINDEL90.00to100.00,INDEL,8,8,1.0000

My question is both known and novel TiTv is zero! I am not sure how to interpret this.

applyvqsr gatk • 101 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by geneart$$40
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