Insane in the vembrane: filtering and transforming VCF/BCF files.
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- Record sourced from PubMed, PMID 36519840.
- Also identified by DOI 10.1093/bioinformatics/btac810 and PMC identifier 9825764.
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Abstract
We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. 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 Python expressions, 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, by using pysam and relying on lazy evaluation. Source code and installation instructions are available at github.com/vembrane/vembrane (doi: 10.5281/zenodo.7003981). Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genetic Variation
- Mental Disorders