Variant Calling in Next Generation Sequencing Data

Abstract

Variant calling in next generation sequencing requires a multistep, sequencing and hypothesis dependent, bioinformatics workflow. Preprocessing is required before variant calling that includes quality control analysis, trimming, alignment, and removal of duplicates. Variant calling algorithms, sequencing source, and depth need to be used to decide on an appropriate variant calling tool. Postprocessing of variant calling formats with annotation, databases, and functional predictions ensures only variants of interest remain. Here we review in detail the bioinformatics workflow, tools, and algorithms need to call quality variants from a variety of next generation sequencing data.