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Weird multi-sample  exome VQSR tranche plot
I am trying to run GATK on a sample of 119 exomes. I followed the GATK guidelines to process the fastq files. I used the following parameters to call the UnifiedGenotyper and VQSR [for SNPs]:
-T UnifiedGenotyper --output_mode EMIT_VARIANTS_ONLY --min_base_quality_score 30 --max_alternate_alleles 5 -glm SNP
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 /media/transcription/cipn/5.pt/ref/hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /media/transcription/cipn/5.pt/ref/1000G_omni2.5.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /media/transcription/cipn/5.pt/ref/dbsnp_135.hg19.vcf.gz -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff -mode SNP
I get a tranche plot, which does not look OK. The "Number of Novel Variants [1000s]" goes from -400 to 800 and the Ti/Tv ratio varies from 0.633 to 0.782 [the attach file link is not working for me and am unable to upload the plot]. Any suggestion to rectify this would be very helpful !