Next-generation sequencing based genetic testing requires proof-of-concept validation with established performance metrics before introducing into the clinical laboratory. The performance metrics evaluated to establish the analytical validity of test results include accuracy, precision, analytical sensitivity, analytical specificity. Precision is typically determined by assessing repeatability and reproducibility. Repeatability (within-run precision) means testing the same sample repeatedly under the same operating conditions (the same people, same time, same place etc.) to evaluate the closeness of agreement between repeated tests. Reproducibility (between-run precision) means the closeness of agreement between the results of measurements when operating conditions are varied(different people, different time etc.). As bioinformatics analysis pipeline is a key component of next-generation sequencing, several guidelines recommended that the bioinformatics analysis pipeline should also be validated. My question is how to evaluate the precision (repeatability and reproducibility) of a bioinformatics analysis pipeline? Or, do I need to evaluate the precision (repeatability and reproducibility) of a bioinformatics analysis pipeline?
So, in a clinical setting, we do test the specificity and sensitivity of our bioinformatics pipeline. This can be done in many ways, most common ones are-
1] run the pipeline on 2-3 previously analysed samples and compare results to see if the expected variants are called
2] run the pipeline using, for example, GIAB samples to compare, again, to see if expected variants are called.
More details are here : Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines