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Weird multi-sample [119] exome VQSR tranche plot

rkanwarrkanwar Posts: 2Member
edited January 2013 in Ask the GATK team


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/ 
-resource:omni,known=false,training=true,truth=false,prior=12.0 /media/transcription/cipn/ 
-resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /media/transcription/cipn/ 
-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 !


Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,568Administrator, Dev admin

    Hi Rahul,

    Sorry it took so long to get back to you. The "attach a file" function is temporarily unavailable, but if you upload a copy of your plot to our FTP server (see here), we'll have a look at it.

    Geraldine Van der Auwera, PhD

  • dcittarodcittaro Posts: 31Member
    edited June 2013

    Actually the same happens to me... take a look to this tranche plot, made for ~60 exomes (GATK 2.4.9)... how should I interpret it?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,568Administrator, Dev admin

    Hi @dcittaro,

    Those do look bad... Can you tell me if those are whole-exomes, or if they're only partial, ie subsets of targets? Also, just checking, but those are only run on SNPs, right? not indels?

    Geraldine Van der Auwera, PhD

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