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!

Powered by Vanilla. Made with Bootstrap.
Register now for the upcoming GATK Best Practices workshop, Nov 7-8 at the Broad in Cambridge, MA. Open to all comers! More info and signup at

Your experience with VQSLOD filtering

dcittarodcittaro Posts: 31Member
edited January 2013 in Ask the GATK team

Dear all,
I have a set of 48 exomes which were analysed according to the best practices (using GATK-2.2-3 and HaplotypeCaller). According to the VQRS I have this first level of "uncertainty":

##FILTER=<ID=VQSRTrancheBOTH90.00to99.00,Description="Truth sensitivity tranche level for BOTH model at VQS Lod: -1.3455 <= x < 2.62">

that sets filter=PASS for variants with VQSLOD >= 2.62.
I also have an external validation of some SNPs, 3 out of 20 have a VQSLOD lower than 2.62 (1.24, .1.37 and 1.69). Now the question: should I trust the validation and set the filter to, say, VQSLOD >= 1.2 or keep the GATK filter? What is your experience about this?



Post edited by Geraldine_VdAuwera on
Sign In or Register to comment.