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High Ti/Tv values

christyvjchristyvj MelbourneMember

Hi there.
We are trying to run VariantRecalibrator (SNP mode) on a set of ~4000 cattle WGS samples (Bos Taurus & Bos Indicus). We are using GATK v3.8. We seem to be getting quite high Ti/Tv values (I have pasted the .tranches file and VariantRecalibrator command below).
We have run the same pipeline on ~3000 Bos Taurus samples and got normal Ti/Tv values of around 1.9 - 2.2.
From my reading, having Ti/Tv too low results in too many false positives. Is it an issue if Ti/Tv is too high? What could be the possible consequence of this? If it is an issue, do you have any suggestions as to how to reduce the Ti/Tv values.
Thank you in advance.

.tranche file:
90.00,0,51671762,0.0000,2.3950,9.6364,VQSRTrancheSNP0.00to90.00,SNP,10453540,9408186,0.9000
99.00,0,78333427,0.0000,2.3309,0.9780,VQSRTrancheSNP90.00to99.00,SNP,10453540,10349004,0.9900
99.90,0,90102373,0.0000,2.3024,-0.9695,VQSRTrancheSNP99.00to99.90,SNP,10453540,10443086,0.9990
100.00,0,166127490,0.0000,2.0857,-39987.6452,VQSRTrancheSNP99.90to100.00,SNP,10453540,10453540,1.0000

VariantRecalibrator command:
java -Xmx450g -jar $GATK -R ${TMPDIR}/ARS-UCD1.2_Btau5.0.1Y.fa -T VariantRecalibrator \
-input Chr1-raw.vcf \
-input ChrY-raw.vcf \
-input ChrMT-raw.vcf \
-input Chr10-raw.vcf \
-input Chr11-raw.vcf \
-input Chr12-raw.vcf \
-input Chr13-raw.vcf \
-input Chr14-raw.vcf \
-input Chr15-raw.vcf \
-input Chr16-raw.vcf \
-input Chr17-raw.vcf \
-input Chr18-raw.vcf \
-input Chr19-raw.vcf \
-input Chr2-raw.vcf \
-input Chr20-raw.vcf \
-input Chr21-raw.vcf \
-input Chr22-raw.vcf \
-input Chr23-raw.vcf \
-input Chr24-raw.vcf \
-input Chr25-raw.vcf \
-input Chr26-raw.vcf \
-input Chr27-raw.vcf \
-input Chr28-raw.vcf \
-input Chr29-raw.vcf \
-input Chr3-raw.vcf \
-input Chr4-raw.vcf \
-input Chr5-raw.vcf \
-input Chr6-raw.vcf \
-input Chr7-raw.vcf \
-input Chr8-raw.vcf \
-input Chr9-raw.vcf \
-input ChrX-raw.vcf \
-resource:HD,known=false,training=true,truth=true,prior=15.0 HD_truth.vcf \
-resource:GGPF250,known=false,training=true,truth=true,prior=15.0 GGPF250_truth.vcf \
-resource:Affy,known=false,training=true,truth=true,prior=12.0 Affy_truth.vcf \
-resource:1000bulls_truth,known=false,training=true,truth=true,prior=12.0 Run7-TauInd-SNP-truth.vcf \
-resource:1000bulls_training,known=false,training=true,truth=false,prior=10.0 Run7-TauInd-SNP-training.vcf \
-an QD -an DP -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -maxNumTrainingData 10000000 \
-mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-recalFile Run7_TAU-IND.AS.recal -tranchesFile Run7_TAU-IND.AS.tranches -rscriptFile Run7_TAU-IND.plots.AS.R

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