SoftGenetics - Software PowerTools for Genetic Analysis


NextGENe-Geneticist Assistant Pipeline supports performance metric reporting of AMP and CAP recommendations.

Use the NextGENe and Geneticist Assistant pipeline to support performance metric reporting of the joint recommendations from the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) for pipeline validation (1).



Table 1: SoftGenetics Support for AMP/CAP Recommended Pipeline Validation

* Currently performed pre-alignment. Post-alignment statistics coming Q4
** Currently separate comparison functions exist. Merging to summary report coming Q4


NextGENe outputs a separate *_PerformanceMetrics.txt file containing the quality metrics listed above. The metrics are also reported within the VCF files exported by NextGENe.


Geneticist Assistant allows the creation of custom quality metric profiles which allows users to determine which metrics are to be reported, to set thresholds for flagging variants, and to define where in the Geneticist Assistant input files the metrics can be found or can be calculated. Default profiles are built-in based on the AMP/CAP recommendations. 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.


Figure 1: Quality metric reporting for a sample in Geneticist Assistant


Figure 2: Quality metric values reported in a sample’s variant table with yellow highlighting for values within warning range and red highlighting for values in failed range.



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

SoftGenetics - Software PowerTools for Genetic Analysis




SoftGenetics - Software PowerTools for Genetic Analysis





SoftGenetics - Software PowerTools for Genetic Analysis

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