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Insane in the vembrane: filtering and transforming VCF/BCF files.
Hartmann, Till; Schröder, Christopher; Kuthe, Elias; Lähnemann, David; Köster, Johannes.
Affiliation
  • Hartmann T; Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany.
  • Schröder C; Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany.
  • Kuthe E; Computer Science XI, TU Dortmund University, Dortmund 44227, Germany.
  • Lähnemann D; Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany.
  • Köster J; Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany.
Bioinformatics ; 39(1)2023 01 01.
Article in En | MEDLINE | ID: mdl-36519840
ABSTRACT

SUMMARY:

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. AVAILABILITY AND IMPLEMENTATION Source code and installation instructions are available at github.com/vembrane/vembrane (doi 10.5281/zenodo.7003981). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genetic Variation / Mental Disorders Type of study: Diagnostic_studies Limits: Humans Language: En Journal: Bioinformatics Journal subject: INFORMATICA MEDICA Year: 2023 Type: Article Affiliation country: Germany
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genetic Variation / Mental Disorders Type of study: Diagnostic_studies Limits: Humans Language: En Journal: Bioinformatics Journal subject: INFORMATICA MEDICA Year: 2023 Type: Article Affiliation country: Germany