bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files
- PMID: 29186339
- DOI: 10.1093/bioinformatics/btx734
bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files
Abstract
Motivation: Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries.
Results: In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk).
Availability and implementation: https://github.com/lindenb/jvarkit.
Contact: pierre.lindenbaum@univ-nantes.fr.
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