What does PCT_MIX from CreateVerifyIDIntensityContaminationMetricsFile mean?
Hello, I'm using IlluminaGenotypingArray from broad's warp repository. There is a task where the Picard tool called CreateVerifyIDIntensityContaminationMetricsFile is executed.
It's output looks like:
## METRICS CLASS picard.arrays.VerifyIDIntensityContaminationMetrics
ID PCT_MIX LLK LLK0
0 0.173228 143346 156881My issue is about the PCT_MIX column. In the CollectHsMetrics doc I can see that:
> Note: Metrics labeled as percentages are actually expressed as fractions!
It is also the case for CreateVerifyIDIntensityContaminationMetricsFile? I ran 96 samples and none of them have this value above 1.
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Hi Lucas Taniguti,
The CollectHsMetrics docs wouldn't necessarily apply here because this is not part of that tool. We looked into Picard's CreateVerifyIDIntensityContaminationMetricsFile and it pulls the statistics from a tool called VerifyIDIntensity, which is not a Picard tool, it looks like it is from this page: https://github.com/gjun/verifyIDintensity. Picard is not doing any further data transformation, so you'll want to reach out to the developers of VerifyIDIntensity for more info.
Best,
Genevieve
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Ok! Thank you Genevieve Brandt (she/her).
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