Multiple Sequence Alignment for Variations Detection

This chapter introduces the current progress in variant calling making use of multiple sequence alignment (MSA) technologies. It briefly talks about four typical variants, including single-nucleotide variants (SNVs), tandem repeats, copy number variations (CNVs), and chromosomal rearrangements. The chapter elaborates six variant callers that use MSA as guidance and provides the common evaluation strategies for comparing and assessing genotyping results by different variant calling tools. It summarizes and point out future directions in this crossing realm of MSA and variant detection. The chapter presents an important bioinformatics application, variant detection, based on the information extracted from the MSA by aligning similar DNA sequences, including short sequencing reads and reference genome sequences. It uses six variant detection tools, containing MUMer, Mugsy, ParSNP, MAQ, Gustaf, and SoftSV, as examples to illustrate the primary ideas about how to employ MSA to infer genetic variants.