Benchmarking and improving the performance of variant-calling pipelines with RecallME

Abstract

Motivation The steady increment of Whole Genome/Exome sequencing and the development of novel NGS-based gene panels requires continuous testing and validation of variant calling pipelines and the detection of sequencing-related issues to be maintained up-to-date and feasible for the clinical settings. State of the art tools are reliable when used to compute standard performance metrics. However, the need for an automated software to discriminate between bioinformatic and sequencing issues and to optimize variant calling parameters remains unmet. The aim of the current work is to present RecallME, a bioinformatic suite that tracks down difficult-to-detect variants as insertions and deletions in highly repetitive regions, thus providing the maximum reachable recall for both single nucleotide variants and small insertion and deletions and to precisely guide the user in the pipeline optimization process. Availability Source code is freely available under MIT license at https://github.com/mazzalab-ieo/recallme RecallME web application is available at https://translational-oncology-lab.shinyapps.io/recallme/ To use RecallME, users must obtain a license for ANNOVAR by themselves. Supplementary information Supplementary data are available at Bioinformatics online.