Bioinformatics Data Skills

Chapter 11. Working with Alignment Data

In Chapter 9, we learned about range formats such as BED and GTF, which are often used to store genomic range data associated with genomic feature annotation data such as gene models. Other kinds of range-based formats are designed for storing large amounts of alignment data—for example, the results of aligning millions (or billions) of high-throughput sequencing reads to a genome. In this chapter, we’ll look at the most common high-throughput data alignment format: the Sequence Alignment/Mapping (SAM) format for mapping data (and its binary analog, BAM). The SAM and BAM formats are the standard formats for storing sequencing reads mapped to a reference.

We study SAM and BAM for two reasons. First, a huge part of bioinformatics work is manipulating alignment files. Nearly every high-throughput sequencing experiment involves an alignment step that produces alignment data in the SAM/BAM formats. Because each sequencing read has an alignment entry, alignment data files are massive and require space-efficient complex binary file formats. Furthermore, modern aligners output an incredible amount of useful information about each alignment. It’s vital to have the skills necessary to extract this information and explore data kept in these complex formats.

Second, the skills developed through learning to work with SAM/BAM files are extensible and more widely applicable than to these specific formats. It would be unwise to bet that these formats ...