{"repo":"sigven/gvanno","free":true,"listed":false,"github":"https://github.com/sigven/gvanno","clone":"git clone https://github.com/sigven/gvanno.git","description":"Generic human DNA variant annotation pipeline","language":"Python","stars":60,"topics":["docker","gene","vep","vcfanno","germline","variant-annotations","vcf","snv","indels","annotation-framework"],"license":"MIT","category":"deployment-docker-iac","readme_excerpt":"gvanno - generic workflow for functional and clinical annotation of human DNA variants Contents - Overview - News - Annotation resources - Getting started - Contact Overview The generic variant annotator ( gvanno ) is a software package intended for simple analysis and interpretation of human DNA variants. Variants and genes are annotated with disease-related and functional associations. Technically, the workflow is developed in Python, and it relies upon Docker / Singularity technology for encapsulation of software dependencies. gvanno accepts query files encoded in the VCF format, and can analyze both SNVs and short insertions or deletions (indels). The workflow relies heavily upon Ensembl's Variant Effect Predictor (VEP), and vcfanno. It produces an annotated VCF file and a file of tab-separated values (.tsv), the latter listing all annotations pr. variant record. Note that if your input VCF contains data (genotypes) from multiple samples (i.e. a multisample VCF), the output TSV file will contain one line/record per sample variant . News - December 29th 2023 - 1.7.0 release - Data updates: ClinVar, GENCODE, GWAS catalog - Software updates: VEP - Improved Singularity support - April 27th 2023 - 1.6.0 release - Added option --oncogenicity annotation - classifies variants according to oncogenicity (Horak et al., Genet Med, 2022) - Data updates: ClinVar, GENCODE, GWAS catalog, CancerMine - Excluded extensive disease associations from the Open Targets Platform - September 26th ","default_branch":null,"files":null,"tree":[],"storefront":"/r/sigven","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/sigven/gvanno/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}