FiNGS: high quality somatic mutations using filters for next generation sequencing
Open Access
- 18 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 22 (1), 1-6
- https://doi.org/10.1186/s12859-021-03995-y
Abstract
Somatic 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. Developed 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. FiNGS 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.Keywords
This publication has 10 references indexed in Scilit:
- Bioconda: sustainable and comprehensive software distribution for the life sciencesNature Methods, 2018
- Comprehensive benchmarking of SNV callers for highly admixed tumor dataPLOS ONE, 2017
- Strelka2: Fast and accurate variant calling for clinical sequencing applicationsPublished by Cold Spring Harbor Laboratory ,2017
- Singularity: Scientific containers for mobility of computePLOS ONE, 2017
- A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencingNature Communications, 2015
- Sensitive detection of somatic point mutations in impure and heterogeneous cancer samplesNature Biotechnology, 2013
- VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingGenome Research, 2012
- The variant call format and VCFtoolsBioinformatics, 2011
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing dataGenome Research, 2010
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009