The current GATK version is 3.7-0
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.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

VQSR, VQSLOD, and indels

mrivasmrivas Member Posts: 1

Hi Mark, Eric -

First, I wanted to thank you guys for providing advice with respect to running VQSR. I am already sold and a huge fan of the method :-).

I was wondering if either of you could comment on VQSLOD and sensitivity filter tranche?
To be more specific, if I set a filter threshold of 99% for sensitivity and VQSLOD < 0 I imagine that probably is not a good idea! However, a VQSLOD of 3 or 5 may be appropriate in the statistical sense, i.e. pretty confident that this is a real variant. Finally, I am thinking we should include VQSLOD in our statistical genetic association mapping methods. I wanted to get a sense from either of you what VQSLOD you would want to completely remove from analysis?

Best Wishes,




  • rpoplinrpoplin Dev Posts: 122 ✭✭✭

    Hey Manny,

    I'm glad that you are enjoying the VQSR. For most of our projects we are generally interested in operating in the regime where sensitivity is at or above 99% so we are happy to tolerate variants in which VQSLOD is near zero in order to get there. We use the VQSLOD simply as a way to rank-order the variants and then decide where to apply that cutoff. If you really want to be sure that your variants have a very low false positive rate then VQSLOD > 3 is a great place to start.

    I would love to see somebody including the VQSLOD in their statistical methods. I think there is a lot of untapped potential there.

    I hope that is helpful. Let me know if you have any other questions.


Sign In or Register to comment.