The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

# Weird multi-sample [119] exome VQSR tranche plot

Member Posts: 2
edited January 2013

Hello,

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]:

UnifiedGenotyper

-T UnifiedGenotyper
--output_mode EMIT_VARIANTS_ONLY
--min_base_quality_score 30
--max_alternate_alleles 5
-glm SNP


VQSR

-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 !

cheers,
Rahul

Post edited by Geraldine_VdAuwera on
Tagged:

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

• Member Posts: 31
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?