Molecular Cloning Fourth Edition, A Laboratory Manual, by Michael R. Green and Joseph Sambrook

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Data Analysis

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VARIANT DISCOVERY ANALYSIS

The essential first step in discovery of variants is the alignment of next-generation sequencing reads with the reference genome for the organism of interest. There are a multitude of alignment algorithms available either from the instrument manufacturing companies, through SourceForge or other open source sites, or by communicating with one's favorite bioinformaticist. Currently, the field favors the use of Burroughs-Wheeler algorithm aligners like bwa. Most alignment algorithms produce a mapping quality metric that should be considered by downstream variant detection algorithms because incorrect mapping to the reference (indicated by a low mapping quality) can be a significant source of false-positive variant detection. As mentioned in the Introduction to this chapter, detection of variants requires different algorithmic approaches, the numbers and types of which are determined by the types of variant one wishes to discover. Several of these approaches are covered in Chapter 8.


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(Limited time special offer.) Molecular Cloning Fourth Edition, A Laboratory Manual, by Michael R. Green and Joseph Sambrook
Molecular Cloning Fourth Edition, A Laboratory Manual, by Michael R. Green and Joseph Sambrook

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