BAMQL: a query language for extracting reads from BAM files

• Published in: BMC bioinformatics Vol. 17; no. 1; p. 305
• Main Authors: Masella, Andre P., Lalansingh, Christopher M., Sivasundaram, Pragash, Fraser, Michael, Bristow, Robert G., Boutros, Paul C.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 11.08.2016; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Base Sequence; Bioinformatics; Biomedical and Life Sciences; Chromosomes; Chromosomes - genetics; Computational biology; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Flags; Funding; Genomes; Internet; Language; Life Sciences; Medical research; Microarrays; Mitochondria - genetics; Perl; Quality; Queries; Query languages; Random variables; Software; User-Computer Interface; Iran; BAM-format; BAMQL; Query language
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-016-1162-y

Background It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream using SAMtools, parses and filters the lines using AWK, then repacks them using SAMtools. This process is tedious and error-prone. In particular, when working with many columns of data, mix-ups are common and the bit field containing the flags is unintuitive. There are several libraries for reading BAM files, such as Bio-SamTools for Perl and pysam for Python. Both allow access to the BAM’s read information and can filter reads, but require substantial boilerplate code; this is high overhead for mostly ad hoc filtering. Results We have created a query language that gathers reads using a collection of predicates and common logical connectives. Queries run faster than equivalents and can be compiled to native code for embedding in larger programs. Conclusions BAMQL provides a user-friendly, powerful and performant way to extract subsets of BAM files for ad hoc analyses or integration into applications. The query language provides a collection of predicates beyond those in SAMtools, and more flexible connectives.