Johannes KösterSep 18, 2025

Our tool #vembrane has a new homepage, providing a high level summary of all the things you can do with it to transform VCF/BCF files via simple Python expressions: https://vembrane.github.io

Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.

Vembrane

Johannes KösterJul 21, 2025
#vembrane, our CLI tool for manipulating VCF/BCF files via Python expressions has gained a new subcommand for sorting. Use it to sort by impact, pathogenicity, frequencies, or any complex Python logic, e.g. for variant prioritization.
https://github.com/vembrane/vembrane/blob/main/docs/sort.md
#genomics #bioinformatics
vembrane/docs/sort.md at main · vembrane/vembrane

vembrane filters VCF records using python expressions - vembrane/vembrane

GitHub
Johannes KösterJun 13, 2025
#vembrane, our tool for filtering and transforming VCF files with easy to read Python expressions has just gained a new subcommand for directly generating #HL7 #FHIR observations from VCF records. Thanks to Till Hartmann for the continued maintenance!
https://github.com/vembrane/vembrane
GitHub - vembrane/vembrane: vembrane filters VCF records using python expressions

vembrane filters VCF records using python expressions - vembrane/vembrane

GitHub
Johannes KösterJan 23, 2023
Our paper on #vembrane is published in @OxfordJournals Bioinformatics. #vembrane is a fast and easy to use tool for filtering BCF/VCF files and converting them to tables. Most importantly, it provides a very powerful Python based query language. Furthermore, it provides proper support for filtering breakends (BND).
https://doi.org/10.1093/bioinformatics/btac810
https://github.com/vembrane/vembrane
Insane in the vembrane: filtering and transforming VCF/BCF files

AbstractSummary. We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filte

OUP Academic