GATK filter question

[kjaja]

I need some advice on interpreting the variants with a GATK Filter flag “TruthSensitivityTranche99.00to99.90” or “TruthSensitivityTranche99.90to100.00”. The question is can I trust these variants or are they likely to be false positive. I have googled around to check for the meaning of these filters with no success. Can some explain what these filter flags mean? Did anyone find these variants to be true positives?

Thanks for help

[gsr9999]

Based on GATK's description of VQSR method, these variants with the annotation 'TruthSensitivityTranche99.90to100.00' seems to be False Positive

http://gatkforums.broadinstitute.org/discussion/39/variant-quality-score-recalibration-vqsr