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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)

Answers

  • AdelaideRAdelaideR Member admin

    @AEGentry, I believe a run-specific Rscript is generated at the same time as the .pdf. Do you have the Rscript in your output?

    Here is an example of code where you can see where the Rscript is generated:

    java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R ${reference} \ -input ${infolder}/${infile} \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 ${hapmap} \ -resource:omni,known=false,training=true,truth=false,prior=12.0 ${omni} \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 ${phase1snp} \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ${dbsnp} \ -an DP \ -an QD \ -an FS \ -an MQRankSum \ -an ReadPosRankSum \ -mode SNP \ -tranche 100.0 \ -tranche 99.9 \ -tranche 99.0 \ -tranche 90.0 \ -numBad 1000 \ -recalFile ${infolder}/recalibrate_SNP.recal \ -tranchesFile ${infolder}/recalibrate_SNP.tranches \ -rscriptFile ${infolder}/recalibrate_SNP_plots.R \ 2>${infolder}/VariantRecalibrator_snp.err

    Take a look at how the Rcode makes the graphs and you should be able to extract that information.

  • AEGentryAEGentry Member

    My script did generate an Rscript, but that script generates the scatterplots and heatmats, not the tranches output.

    This is the tranches output I'm talking about:

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