Insane in the vembrane: filtering and transforming VCF/BCF files

Abstract

Data from sequencing of DNA or RNA samples is routinely scanned for variation. Such variation data is stored in the standardized VCF/BCF format with additional annotations. Analyses of variants usually involve steps where filters are applied to narrow down the list of candidates for further analysis. A number of tools for this task exist, differing in functionality, speed, syntax and supported annotations. Thus, users have to switch between tools depending on the filtering task, and have to adapt to the respective filtering syntax. We present vembrane as a command line VCF/BCF filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. To this end, vembrane exposes the VCF/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by arbitrary Python expressions over (combinations of) annotations, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, thanks to pysam, a Python wrapper around htslib, and by relying on Pythons lazy evaluation. Availability and ImplementationSource code and installation instructions are available at github.com/vembrane/vembrane, DOI: 10.5281/zen-odo.7003981.