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Problem understanding construction of Tranches Plots
sp580
GermanyMember ✭
Hello!
I must be missing a fundamental concept about VQSR, because I cannot figure out how false positives are defined in the construction of the tranches plot.
First, I understand a tranche as a subset of the original raw sites, in which sites PASS if they are above a particular VQSLOD score that allows to keep N% of the sites in the truth set. From this, all sites in the tranche must have FILTER=PASS, and some of those sites will be novel because they do not appear in any of the resources provided.
When constructing the tranches plot, only novel sites are considered.
So, if in order to be in the tranche, a site must have PASSed filtering by VQSLOD score, then where do the tranche specific false positives come from?
This question is derived from a previous post where it was indicated that
All the SNPs that are found are considered "positives" because they were found by earlier stages of analysis. "True" vs "False" positives is simply referring to whether they pass the VQSR filter in a given tranche.
Is there a stage in the analysis that I am not considering?
Thanks
Best Answer
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gauthier
✭✭✭
Hi @sp580 ,
The way we represent the tranches has changed a lot since the first release of VQSR, so the documentation can be spotty and contradictory. I know from looking at the code that the false positives are estimated based on the calculated Ti/Tv of the variants in that tranche compared with the target Ti/Tv argument for VariantRecalibrator (which defaults to 2.15 https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php#--target-titv) I'm honestly not sure where the equation to estimate the FPR comes from (see titvFPest in https://github.com/broadinstitute/gatk/blob/master/src/main/resources/org/broadinstitute/hellbender/tools/walkers/vqsr/plot_Tranches.R), but it was written a long time ago and I wouldn't be surprised if it was a heuristic based on comparing known 1000G variants recalibrated against CEU trio variants or something like that. Sorry for the hand wavy answer, but hopefully that makes intuitive sense.
-Laura
Answers
Hi @sp580 ,
The way we represent the tranches has changed a lot since the first release of VQSR, so the documentation can be spotty and contradictory. I know from looking at the code that the false positives are estimated based on the calculated Ti/Tv of the variants in that tranche compared with the target Ti/Tv argument for VariantRecalibrator (which defaults to 2.15 https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php#--target-titv) I'm honestly not sure where the equation to estimate the FPR comes from (see titvFPest in https://github.com/broadinstitute/gatk/blob/master/src/main/resources/org/broadinstitute/hellbender/tools/walkers/vqsr/plot_Tranches.R), but it was written a long time ago and I wouldn't be surprised if it was a heuristic based on comparing known 1000G variants recalibrated against CEU trio variants or something like that. Sorry for the hand wavy answer, but hopefully that makes intuitive sense.
-Laura
Thanks @gauthier
this is the one piece of information that I need and I think I got it now, but just to be sure:
Blue = set of novel variants with a TiTv similar to the expected TiTv, thus TP
Orange = set of novel variants that depart significantly from the expected TiTv, thus FP
Did I get it right?
Yes, @sp580 , that's the gist of it. Of course we're not actually assessing each variant as being a TP or FP, but using the fact that the TiTv for FPs is much lower (it would be 1/3 if it were totally random, but artifacts are not necessarily random) than for TPs to estimate what proportion of variants have the good TiTv and what proportion have the bad based on the calculated TiTv for that tranche.