{"id":42076983,"url":"https://github.com/zhanxw/vcf2geno","last_synced_at":"2026-01-26T09:35:59.428Z","repository":{"id":7026508,"uuid":"8299446","full_name":"zhanxw/vcf2geno","owner":"zhanxw","description":"Convert Variant Call Format (VCF) file to genotype file","archived":false,"fork":false,"pushed_at":"2013-12-08T02:03:05.000Z","size":1196,"stargazers_count":6,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2023-03-10T21:42:26.732Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zhanxw.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-02-19T21:05:45.000Z","updated_at":"2021-08-22T06:28:08.000Z","dependencies_parsed_at":"2022-09-11T23:21:44.086Z","dependency_job_id":null,"html_url":"https://github.com/zhanxw/vcf2geno","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"purl":"pkg:github/zhanxw/vcf2geno","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zhanxw%2Fvcf2geno","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zhanxw%2Fvcf2geno/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zhanxw%2Fvcf2geno/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zhanxw%2Fvcf2geno/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zhanxw","download_url":"https://codeload.github.com/zhanxw/vcf2geno/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zhanxw%2Fvcf2geno/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28772914,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-26T08:38:24.014Z","status":"ssl_error","status_checked_at":"2026-01-26T08:38:22.080Z","response_time":59,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2026-01-26T09:35:58.775Z","updated_at":"2026-01-26T09:35:59.418Z","avatar_url":"https://github.com/zhanxw.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"vcf2geno\n=========\n\nConvert VCF files to genotype file and site file.\n\nInput File\n----------\n\nVcf2geno takes VCF files. They can be in plain text or GZIP/BGZIP compressed formats.\n\nOutputs\n-------\nVcf2geno generates two sets of files: prefix.geno and prefix.site where ''prefix'' is the given parameter to ''--out''.\n\nA .geno file is shown below:\n\n    X1  X1  0   -9  0   0   0   2   2   2   2   2   2\n    X2  X2  -9  -9  0   0   0   2   2   2   2   2   2\n    X3  X3  0   -9  0   0   0   2   2   2   2   2   2\n    X4  X4  0   -9  0   0   0   2   2   2   2   2   2\n    X5  X5  0   -9  0   0   0   2   2   1   2   2   2\n    X6  X6  0   -9  0   0   0   2   2   2   2   2   -9\n\nThe first and second columns are sample IDs copied from the header of VCF files.\nFrom column 3 till the last the column, they are individual level genotype converted from VCF files.\n\nA .site file is shown below:\n\n    CHROM   POS ID  REF ALT\n    1   10  1:10    A   T\n    1   20  1:20    G   C\n    1   30  1:30    C   A\n    1   40  1:40    A   C\n    1   10000   1:10000 G   C\n    1   20000   1:20000 T   A\n    4   5000    4:5000  A   T\n    4   6000    4:6000  C   T\n    X   800 X:800   A   C\n    X   900 X:900   A   T\n    X   1000    X:1000  T   G\n\nThe content of .site file begins with a header line, and thus the content part from the second line is chromosome, positions, reference alleles and alternative alleles.\n\nOptions\n-------\n\nVcf2geno provides sample selection options and range selection options.\n\nThere are four options to include/exclude samples:\n\n    --peopleIncludeID, --peopleExcludeID: specify which samples are included/excluded in conversion \n\ne.g. --peopleIncludeID X1,X2,X3 will convert only 3 people during conversion if input VCF file contains these three samples.\n\n    --peopleIncludeFile, --peopleExcludeFile: specify a file to include/exclude samples. \n    \nEach line of the file should be a sample ID.\n\nThere are two options to specify regions. You can convert part of the VCF file using this option, however, your input file must be indexed by TABIX.\n\n    --rangeList: this options enable you to specify a range by hand. \ne.g. --rangeList 1:100-200. Note your chromosome name in the command line should be consistent to the content of the VCF file (e.g. both do not have 'chr' prefix).\n\n    --rangeFile: this option specifies range using an external file. \nEach line of the file should specify a range, e.g. '1:100-200', or alternatively three columns '1 100 200'. \n\n    --updateID: this option specifies an external file to update the sample ID in the input VCF file.\nThis file should have three columns. The first columns are sample ID used in the input VCF file. The second and third columns are the family ID and individual ID. \nvcf2geno will update the IDs in the VCF to the family ID and individual ID in the outputted genotype file.\n \nExample\n-------\n\nUnder the \"exampleVCF\" folder, you can file example.vcf.gz. This is an indexed VCF file.\nBasic usage of extracting all samples across all regions:\n\n    ../vcf2geno --inVcf example.vcf.gz --out test\n\nConvert sample X1 from range 1:20-30:\n\n    ../vcf2geno --inVcf example.vcf.gz --rangeList 1:20-30 --peopleIncludeID X1 --out test\n\nExtract all samples and update sample IDs using a separate file ''test.updateId'':\n\n    ../vcf2geno --inVcf example.vcf.gz --out test --updateID test.updateId \n\n \nContact\n-------\nQuestions or comments should be sent to Xiaowei Zhan\n([zhanxw@umich.edu](mailto:zhanxw@umich.edu \"mailto:zhanxw@umich.edu\"))\nor Chaolong Wang\n([chaolong@umich.edu](mailto:chaolong@umich.edu \"mailto:chaolong@umich.edu\"))\nor Goncalo Abecasis\n([goncalo@umich.edu](mailto:goncalo@umich.edu \"mailto:goncalo@umich.edu\"))\n\n\n\n\n[![Bitdeli Badge](https://d2weczhvl823v0.cloudfront.net/zhanxw/vcf2geno/trend.png)](https://bitdeli.com/free \"Bitdeli Badge\")\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzhanxw%2Fvcf2geno","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzhanxw%2Fvcf2geno","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzhanxw%2Fvcf2geno/lists"}