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VQSR, VQSLOD, and indels

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 Member ✭✭✭

    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.


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