VCFPy
VCFPy: a Python 3 library with good support for both reading and writing VCF - Published in JOSS (2016)
cutevariant
A standalone and free application to explore genetics variations from VCF file
https://github.com/brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
divbrowse
A web application for interactive visualization and exploratory data analysis of variant call matrices
https://github.com/bigbio/py-pgatk
Python tools for proteogenomics analysis toolkit
https://github.com/brentp/peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
https://github.com/brentp/indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
https://github.com/brentp/hts-nim-tools
useful command-line tools written to showcase hts-nim
https://github.com/cnag-biomedical-informatics/beacon2-cbi-tools
Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)
https://github.com/cnag-biomedical-informatics/pheno-ranker
Pheno-Ranker is a tool for comparing phenotypic data structured in JSON/YAML format, such as Beacon v2 Models or Phenopackets v2, as well as CSV.
PopGenHelpR
PopGenHelpR is an R package that estimates commonly used population genomic statistics and generates publication quality figures.
helical
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
https://github.com/arvkevi/clinanno
Annoate a .vcf file with publicly-available data