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 156881
My 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.
Please sign in to leave a comment.