Phred QUAL Score filter

This filter can be added to filter chains in the software to filter the by the Phred QUAL score. Phred QUAL scores are defined as a property which is logarithmically related to the base-calling error probabilities.

The filter returns Phred Qual scores for variants calls in the samples and is calculated as follows.

  • For variants, the score is computed by the posterior probability that the sample variant allele frequency is greater than the minimum allele-frequency that is specified for the variant type.

  • For reference calls, the score is computed by posterior probability that the variant allele frequency is below this threshold.

Posterior probability computed conditional on the reads observed, includes sampling variability.

Filter conditions include the ability to set a range from 0.0 to 1000000.0. In addition, the range boundary values can be included or excluded, and unannotated variants can be included or excluded in filtered analysis results.