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bioRxiv · 10.1101/643163

Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays.

Utiramerur, S.·Krishnan, V.·Ng, Z.·Datta, S.·Synder, M.·Ashley, E.
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Abstract

Benchmarking the performance of complex analytical pipelines is an essential part of developing Laboratory Developed Assays (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) Consortium have enabled the evaluation of analytical methods. However, the performance of such methods is not uniform across the different regions of the genome/exome and different variant types and lengths. Here we present a scalable and reproducible, cloud-based benchmarking workflow that can be used by clinical laboratories to rapidly access and validate the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples.

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Utiramerur, S., Krishnan, V., Ng, Z., Datta, S., Synder, M., Ashley, E.. 2019-05-20. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays.. https://doi.org/10.1101/643163

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