I understand it has been a long time since this discussion here, but this has raised a similar question in me.
I have the tranches file generated from VQSR, however based on the tranch plot itself, I would pick 99.9 tranch to go to applyVQSR, as the TP is better in the 99.9 tranch based on the plot ,across cumulative and Tranch specific, TP. However the VQSLOD for that specific tranch is negative. So ,
- do I need to address this issue of picking a tranch cutoff based on tranch plot or VQSLOD score before applyVQSR? or do i just go ahead with apply VQSR and then filter based on VQSLOD?
Lost here, Any suggestions appreciated!
- Also the TiTv is lower than what is suggested by GATK for a WES which is indicative of high FP.