{"repo":"bioinfo-chru-strasbourg/howard","free":true,"listed":false,"github":"https://github.com/bioinfo-chru-strasbourg/howard","clone":"git clone https://github.com/bioinfo-chru-strasbourg/howard.git","description":"Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery","language":"Python","stars":13,"topics":["genetic","variations","annotation","vcf","annovar","snpeff","duckdb","parquet","prioritization"],"license":"AGPL-3.0","category":"data-pipelines","readme_excerpt":"HOWARD HOWARD - Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery HOWARD annotates and prioritizes genetic variations, calculates and normalizes annotations, explore data with an interactive terminal, translates files in multiple formats (e.g. vcf, tsv, Parquet), generates variants statistics, and provides a graphical user interface. HOWARD annotation tool is primarily based on a built-in Parquet annotation method and external tools such as BCFTOOLS, ANNOVAR, snpEff, Exomiser, and Splice (see documentation, automatically downloaded if needed). Parquet annotation uses annotation databases in VCF or BED format, in multiple file formats: Parquet/DuckDB, VCF, BED, TSV, CSV, TBL, JSON. HOWARD calculation tool processes variants information to calculate new information, such as harmonizing allele frequency (VAF), extracting nomenclature (transcript, cNomen, pNomen etc.) from HGVS fields with an optional list of personalized transcripts, generating VaRank format barcodes. HOWARD prioritization tool uses profiles to flag variants (passed/filtered), calculate a prioritization score, and automatically generate a comment for each variant (e.g., 'polymorphism identified in dbSNP, associated with Lung Cancer, found in ClinVar database'). Prioritization profiles are defined in a configuration file. A profile is defined as a list of annotation/value pairs, using wildcards and comparis","default_branch":null,"files":null,"tree":[],"storefront":"/r/bioinfo-chru-strasbourg","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/bioinfo-chru-strasbourg/howard/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."}