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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?