{"id":22295454,"url":"https://github.com/maehler/vcfsubsample","last_synced_at":"2025-03-25T22:27:37.055Z","repository":{"id":79451621,"uuid":"84458981","full_name":"maehler/vcfsubsample","owner":"maehler","description":"Subsample a VCF file in order to fix the minor allele frequency across SNPs","archived":false,"fork":false,"pushed_at":"2020-06-11T09:12:32.000Z","size":21,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-30T19:47:58.572Z","etag":null,"topics":["bioinformatics","genomics","genotype","vcf"],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/maehler.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}},"created_at":"2017-03-09T15:41:57.000Z","updated_at":"2020-06-11T09:12:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"2a58af5f-487c-408d-bf29-9205e48e8ddf","html_url":"https://github.com/maehler/vcfsubsample","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maehler%2Fvcfsubsample","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maehler%2Fvcfsubsample/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maehler%2Fvcfsubsample/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maehler%2Fvcfsubsample/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/maehler","download_url":"https://codeload.github.com/maehler/vcfsubsample/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245552771,"owners_count":20634252,"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","genomics","genotype","vcf"],"created_at":"2024-12-03T17:42:11.804Z","updated_at":"2025-03-25T22:27:37.013Z","avatar_url":"https://github.com/maehler.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Subsample genotype data\n\nIn genome wide association (GWA) studies a recurring problem is differences in statistical power due to sample sizes and rare sequence variants. One way to account for this is to subsample the data in order to \"lock\" the minor allele frequency (MAF) in the data set, *i.e.* all SNPs will have the same MAF.\n\nThis is a tool that will help with this subsampling.\n\n## Requirements\n\n- CMake\n- htslib\n- argp\n\nOn Mac, argp can can be installed through Homebrew with the argp-standalone formula.\n\n## Build\n\n```bash\ngit clone --recursive https://github.com/maehler/vcfsubsample\ncd vcfsubsample\nmkdir build\ncd build\ncmake ..\nmake\nmake install\n```\n\n## Usage\n\n```\n\u003e vcfsubsample --help\nUsage: vcfsubsample [OPTION...] VCF\nvcfsubsample -- subsample a VCF file in order to fix the minor allele frequency\nacross SNPs\n\n     --exact-samples        Subsample to exactly --min-samples\n     --keep-missing         Keep SNPs for which subsampling is not possible\n     --maf=FLOAT            Target MAF to aim for\n     --margin=FLOAT         Allow target MAF within this margin\n     --max-mgf=FLOAT        Maximum genotype frequency to allow for each SNP\n     --min-samples=N        Minimum number of samples to allow\n     --samplenames          Output names of suggested samples to use for\n                            subsampling instead of the number of genotypes of\n                            each class\n -?, --help                 Give this help list\n     --usage                Give a short usage message\n -V, --version              Print program version\n\nReport bugs to \u003cniklas.mahler@gmail.com\u003e.\n```\n\nGenotype data can be read from stdin by using `-` for the VCF filename.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaehler%2Fvcfsubsample","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaehler%2Fvcfsubsample","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaehler%2Fvcfsubsample/lists"}