BAMQL: a query language for extracting reads from BAM files

BMC Bioinformatics

Software

Michael Fraser¹  Robert G. Bristow²  Christopher M. Lalansingh³  Andre P. Masella³  Pragash Sivasundaram³  Paul C. Boutros⁴ 

[1] Ontario Cancer Institute, Princess Margaret Cancer Centre/University Health Network, Toronto, Canada;Ontario Cancer Institute, Princess Margaret Cancer Centre/University Health Network, Toronto, Canada;Department of Medical Biophysics, University of Toronto, Toronto, Canada;Department of Radiation Oncology, University of Toronto, Toronto, Canada;Ontario Institute for Cancer Research, Suite 510, 661 University Avenue, M5G 0A3, Toronto, Canada;Ontario Institute for Cancer Research, Suite 510, 661 University Avenue, M5G 0A3, Toronto, Canada;Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada;Department of Medical Biophysics, University of Toronto, Toronto, Canada;

关键词: BAMQL;    Query language;    BAM-format;   

DOI  :  10.1186/s12859-016-1162-y

 received in 2016-04-08, accepted in 2016-07-21,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundIt 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.ResultsWe 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.ConclusionsBAMQL 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.

【 授权许可】

CC BY   
© The Author(s) 2016