Quality Metrics

Geneticist Assistant allows the creation of custom quality metric profiles which allow users to determine which metrics are to be reported, set thresholds for flagging variants, and define where in the Geneticist Assistant input files the metrics can be found or can be calculated. Metrics are reported in sample level and variant level tables with highlighting for metrics that are within the failure or warning range based on the user-defined thresholds.

Sample Quality Metric Report: Values in failed range are highlighted in red while values in the warning range are highlighted in yellow

Quality Metric Values in Sample Variant Table: Variant level metrics are reported in the sample variant table with red and yellow highlighting for values in the failed and warning ranges, respectively

This function provides support for performance metric reporting based on the joint recommendations from the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) for pipeline validation (1).


[1] Roy, Somak, et al. “Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines.” The Journal of Molecular Diagnostics (2018).