Chapter 29

A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data

Jacob Porter; Jonathan Berkhahn; Liqing Zhang    Department of Computer Science, Virginia Tech, Blacksburg, VA, USA

Abstract

Insertions and deletions (indels) are one of the most common class of mutations in the human genome. Correctly detecting and identifying indels is important in the study of human genetics and disease. In this chapter, we evaluated the precision and recall of combinations of read mapping and indel calling software on calling short and longer indels with variable read coverage and read length on simulated data. We examined the popular read mappers BFAST, Bowtie2, BWA, and SHRIMP, and the indel callers Dindel, ...

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