November 2017
Intermediate to advanced
472 pages
11h 21m
English
book
Basic Applied Bioinformatics
by Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
Content preview from Basic Applied Bioinformatics
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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), ...
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