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Truth-sensitivity-filter-level in ApplyVSQR

Sarah61Sarah61 PakistanMember

Iam doing WES. I have done VariantRecalibrator step. I have used ApplyVSQR and got this result

chr1 13273 rs531730856 G C 1023.88 VQSRTrancheSNP99.90to100.00 AC=6;AF=0.250;AN=24;AS_InbreedingCoeff=0.6320;AS_QD=12.80;BaseQRankSum=0.551;DB;DP=177;ExcessHet=0.0742;FS=12.051;InbreedingCoeff=0.6320;MLEAC=6;MLEAF=0.250;MQ=31.37;MQRankSum=0.589;NEGATIVE_TRAIN_SITE;QD=12.80;ReadPosRankSum=1.08;SOR=2.124;VQSLOD=-6.853e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:36,27:63:99:647,0,878 0/0:29,0:29:81:0,81,1215 1/1:0,4:4:12:116,12,0 ./.:0,0:0:.:0,0,0 1/1:0,4:4:12:129,12,0 0/0:8,0:8:24:0,24,246 ./.:0,0:0:.:0,0,0 0/0:19,0:19:51:0,51,765 0/1:1,8:9:0:197,0,0 0/0:10,0:10:27:0,27,405 0/0:4,0:4:12:0,12,131 0/0:5,0:5:15:0,15,204 0/0:16,0:16:39:0,39,585 ./.:0,0:0:.:0,0,0 0/0:6,0:6:15:0,15,225
chr1 13417 rs777038595 C CGAGA 1426.83 . AC=4;AF=0.167;AN=24;AS_InbreedingCoeff=0.2256;AS_QD=19.55;BaseQRankSum=-1.620e-01;DB;DP=154;ExcessHet=0.7463;FS=0.000;InbreedingCoeff=0.2256;MLEAC=5;MLEAF=0.208;MQ=21.09;MQRankSum=0.666;QD=19.55;ReadPosRankSum=-6.660e-01;SOR=1.179 GT:AD:DP:GQ:PL 0/1:20,22:42:99:709,0,1128 0/0:17,0:17:45:0,45,675 1/1:0,8:8:24:280,24,0 0/0:11,0:11:27:0,27,405 ./.:4,0:4:.:0,0,0 0/0:5,0:5:15:0,15,182 ./.:0,0:0:.:0,0,0 0/0:16,0:16:42:0,42,630 0/1:9,14:23:99:501,0,464 0/0:4,0:4:12:0,12,141 0/0:9,0:9:21:0,21,315 0/0:3,0:3:0:0,0,41 0/0:7,0:7:21:0,21,285 ./.:0,0:0:.:0,0,0 0/0:3,0:3:0:0,0,41
This is my command
gatk ApplyVQSR -R new_hg38.fa \
-V allsample.vcf \
-O output.snps.vcf \
--truth-sensitivity-filter-level 99.0 \
--tranches-file output.snp.tranches \
--recal-file output.snp.recal \
-mode SNP

Can you please guide me which truth-sensitivity-filter-level should I use?


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