Basic Applied Bioinformatics

CHAPTER 40Single Nucleotide Polymorphism (SNP) Mining Tools

Mir Asif Iquebal, Sarika and D Kumar

CABiN, ICAR‐IASRI, New Delhi, India

40.1 INTRODUCTION

There exist genetic variations among individuals of all organisms, and these genetic variations make individuals look phenotypically different. Single nucleotide polymorphisms (SNPs) are considered the simplest and most abundant type of genetic variations in the genome of organisms. SNPs are the markers of choice in most species for genome‐wide association studies (GWAS), phylogenetic analysis, marker‐assisted selection and genomic selection (Liu et al. 2013). They are the genetic markers of choice due to their high density and stability, and the highly automated techniques which are available for detection of SNPs (Kerstens et al., 2009).

Numerous tools are available online for mining SNPs computationally. SNP mining in NGS data has been well documented using two online open source tools: Stacks (Catchen et al., 2011; Ogden et al., 2013) and GATK (DePristo et al., 2011).

40.2 OBJECTIVE

To learn about SNP mining using Stacks, the Burrows–Wheeler algorithm (BWA) aligner, the Genome analysis toolkit (GATK) and Samtools.

40.3 PROCEDURE

We will learn to install and run the tools STACKS, BWA, GATK, Samtools, and so on, to mine SNPs in given nucleotide sequences.

40.3.1 Stacks

This is a program to study population genetics, and it is designed to work with any restriction‐enzyme‐based data, such as GBS (Genotyping by Sequencing), ...