NextGENe supports 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) by exporting many of the recommended metrics in both VCF output as well as a separate summary text file output automatically for any alignment project. See below for a list of performance metrics reported.
Table 1: List of CAP/AMP quality metrics supported by NextGENe
When importing NextGENe VCF files including these performance metrics, Geneticist Assistant can be used for further review of performance metric data. Geneticist Assistant allows the creation of custom quality metric profiles, which allows users to: determine which metrics are to be reported, set thresholds for flagging variants 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.
References:
[1] Roy, Somak, et al. “Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines.” The Journal of Molecular Diagnostics (2018).
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