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Mutation Analysis

Identifying known mutations, and discovering novel genomic mutations, has been one of the most popular applications of next generation sequencing (NGS) technologies.

This case study, where we describe several approaches for performing identification of mutations, including single nucleotide polymorphisms (SNPs), short insertions and deletions (INDELs), as well as other genomic variations such as intermediate and long INDELs, tandem duplications, substitutions and inversions.

The study includes a comparison of different mutation discovery algorithms, an outline of the issues of mutation analysis specific to haploid organisms, and an overview of the process of mutation detection using RNASeq data.


In most cases, there are four steps for detecting SNPs and short INDELs using NGS data:

    • The raw samples should be examined using a quality assessment tool. For this purpose, we tend to rely on FASTQC, which provides easy-to-use numeric and graphical assessment of each sample‚Äôs quality.
    • The samples should be mapped (aligned) to a reference genome. Several tools are available but, unfortunately, these tools do not always produce equivalent results. For more information, please see our previous case study, Impact of Mapping Algorithms on SNP Discovery that compared SNP detection results using 3 different mapping algorithms: bowtie, bowtie2 and BWA.
    • After mapping, we recommend performing assessment of coverage across either the entire genome (if conducting whole genome mutation analysis) or across the specific enrichment subset (in most cases, this subset is either the exome or a gene enrichment panel).
    • Once the samples are mapped, detection of SNPs and INDELs can be performed using several available algorithms. In this Case Study, we take a look at the differences between two of the most popular tools, GATK and Samtools.

For the complete results of the analysis of sequence data, download the white paper here.

If you have questions about the study, or how Lumenogix NGS can help your organization manage and analyze NGS data, please Contact Us directly.