{"id":15893470,"url":"https://github.com/multimeric/improvar","last_synced_at":"2025-06-17T15:34:14.420Z","repository":{"id":85377244,"uuid":"129852410","full_name":"multimeric/Improvar","owner":"multimeric","description":"A python script for generating sample VCF data based on a template VCF","archived":false,"fork":false,"pushed_at":"2018-05-01T03:50:01.000Z","size":26,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-02T17:51:30.073Z","etag":null,"topics":["bioinformatics","variant-calling","vcf"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/multimeric.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-04-17T05:45:47.000Z","updated_at":"2020-10-06T06:10:39.000Z","dependencies_parsed_at":null,"dependency_job_id":"e1bd3b99-adf1-44dd-90ef-d834476f9090","html_url":"https://github.com/multimeric/Improvar","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/multimeric/Improvar","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FImprovar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FImprovar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FImprovar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FImprovar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/multimeric","download_url":"https://codeload.github.com/multimeric/Improvar/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FImprovar/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260388588,"owners_count":23001552,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","variant-calling","vcf"],"created_at":"2024-10-06T08:10:57.427Z","updated_at":"2025-06-17T15:34:09.395Z","avatar_url":"https://github.com/multimeric.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Improvar\n\n`improvar` generates fake VCF files using another VCF as a template. This is useful for generating\ntest data in bioinformatics situations. In particular, `improvar` generates values for all the fields\nlisted in the header, even if your template didn't, allowing you to test your analysis pipeline with\nmore completely.\n\n## Installation\nInstall `improvar` using:\n```bash\npip install 'git+https://github.com/TMiguelT/Improvar#egg=improvar'\n```\n\nNote that `improvar` will only work on Python 3.6 and above\n\n## Usage\n`improvar` installs a command-line utility called `improvar`. Its usage is as follows:\n```\nusage: improvar [-h] [--num-variants NUM_VARIANTS]\n                [--gt-opts {GenotypeOption.HOM_REF,GenotypeOption.HOM_ALT,GenotypeOption.HET}]\n                [--include-contig INCLUDE_CONTIG]\n                [--exclude-contig EXCLUDE_CONTIG]\n                template_vcf\n\nGenerates a fake VCF based on another VCF's header\n\npositional arguments:\n  template_vcf          The VCF to base the generated data off\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --num-variants NUM_VARIANTS, -n NUM_VARIANTS\n                        Number of variants to print\n  --gt-opts {GenotypeOption.HOM_REF,GenotypeOption.HOM_ALT,GenotypeOption.HET}\n                        Constraints to apply when generating genotype. Leave\n                        empty to generate entirely random genotypes. Use \"het\"\n                        to generate only heterozygotes (e.g. 0|1), use \"hom-\n                        ref\" to generate only homozygous referencegenotpyes\n                        (e.g. 0|0), and use \"hom-var\" to generate only\n                        homozygous variant genotypes (e.g. 1|1)\n  --include-contig INCLUDE_CONTIG\n                        Only output contigs whose name matches this regex\n                        pattern\n  --exclude-contig EXCLUDE_CONTIG\n                        Do not output contigs whose name matches this regex\n                        pattern\n```\n\n`improvar` prints the generated VCF to stdout, so you can pipe the results of this program to a file\nor to other VCF processing tools","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultimeric%2Fimprovar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmultimeric%2Fimprovar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultimeric%2Fimprovar/lists"}