FiNGS: high quality somatic mutations using filters for next generation sequencing

BackgroundSomatic variant callers are used to find mutations in sequencing data from cancer samples. They are very sensitive and have high recall, but also may produce low precision data with a large proportion of false positives. Further ad hoc filtering is commonly performed after variant calling and before further analysis. Improving the filtering of somatic variants in a reproducible way represents an unmet need. We have developed Filters for Next Generation Sequencing (FiNGS), software written specifically to address these filtering issues.ResultsDeveloped and tested using publicly available sequencing data sets, we demonstrate that FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.ConclusionsFiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

Automated summary

FiNGS is a software developed to improve the precision of variant caller outputs for somatic variants, with demonstrated reliability and better performance than other tools for the same task. It provides researchers with a simple, configurable, and reproducible tool for filtering somatic variants in sequencing data.