{"id":18989828,"url":"https://github.com/cdcgov/snpeffr","last_synced_at":"2026-03-02T11:01:58.003Z","repository":{"id":68367964,"uuid":"578723537","full_name":"CDCgov/snpeffr","owner":"CDCgov","description":"R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net","archived":false,"fork":false,"pushed_at":"2025-03-12T20:53:55.000Z","size":84467,"stargazers_count":1,"open_issues_count":0,"forks_count":3,"subscribers_count":5,"default_branch":"dev","last_synced_at":"2025-09-09T23:38:00.740Z","etag":null,"topics":["clitool","myco","rpackage","snpeff"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CDCgov.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"code-of-conduct.md","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,"zenodo":null}},"created_at":"2022-12-15T18:22:31.000Z","updated_at":"2025-07-29T13:29:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"4690233f-1cc5-4035-a7a4-873311d16db0","html_url":"https://github.com/CDCgov/snpeffr","commit_stats":{"total_commits":13,"total_committers":2,"mean_commits":6.5,"dds":"0.23076923076923073","last_synced_commit":"ccce198bff863d018d10fbd65bdc0436f8997857"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":"CDCgov/template","purl":"pkg:github/CDCgov/snpeffr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fsnpeffr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fsnpeffr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fsnpeffr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fsnpeffr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","download_url":"https://codeload.github.com/CDCgov/snpeffr/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fsnpeffr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29999221,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-02T09:59:02.300Z","status":"ssl_error","status_checked_at":"2026-03-02T09:59:02.001Z","response_time":60,"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":["clitool","myco","rpackage","snpeff"],"created_at":"2024-11-08T17:08:04.007Z","updated_at":"2026-03-02T11:01:57.985Z","avatar_url":"https://github.com/CDCgov.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# snpeffr\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\nThe goal of the snpeffr package is to filter and parse outputs generated by snpeffr for MDB/Fungi Net.\nIt depends on the R packages `data.table` and `R.utils`. If using the command line \nscript included, you will also need the package `docopt`.\n\n**Note that development happens on the dev branch to manage versions. The master branch is the legacy version of snpeffr maintained for backwards compatibility with\nolder versions of [mycosnp-nf](https://github.com/CDCgov/mycosnp-nf).**\n\n## Installation\n\nYou can install the development version of snpeffr like so:\n\n``` r\n# if remotes not installed, then install the pkg\nif(!require(remotes)) install.packages(\"remotes\")\n\nremotes::install_github(\"CDCgov/snpeffr@dev\")\n\n```\nOr if you don't have git set up:\n\n``` r \n# install from zip location so no need for git\nremotes::install_url(\"https://github.com/CDCgov/snpeffr/archive/refs/heads/dev.zip\")   \n\n```\n\n## Example\n\nYou can test out the function on the example data provided:\n\n```{r example}\nlibrary(snpeffr)\n\n# path to example vcf included in package \n# replace with path to your vcf output if running on your own example\nvcf_exe \u003c- file.path(path.package(\"snpeffr\"), \"vcf-filter_ann_mod.vcf.gz\")\n\n# basic example\nout \u003c- snpeffr(vcf_path = vcf_exe)\n\nhead(out)\n\n# to see function documentation/help for more details on the arguments and output\n?snpeffr\n\n```\n\n## Command-line script\n\nYou can also use a command line version of this script at [inst/snpeffr.R](inst/snpeffr.R).\n\nDownload the file and from the directory where it's downloaded, run:\n\n```\n./snpeffr.R -f path_to_vcf\n\n```\n\nTo get help and options for the command line version:\n\n```\n./snpeffr.R -h\n\n```\nWhich will display the following help message:\n```\nParse snpeff output to summary of mutations at positions of interest\n\nUsage:\n    snpeffr.r [--fpath=FPATH] [--pos=POS] [--genes=GENES] [-exc=EXCL] [-out=OUT]\n\nOptions:\n    -v, --version           Show version.\n    -f FPATH --fpath=FPATH  path to input vcf file from snpeff\n    -p POS --pos=POS        format as named comma separated list\n                            of positions (no spaces), i.e. see default\n                            [default: fks1_hs1=221637:221663,fks1_hs2=223782:223805,fks1_hs3=221805:221807]\n    -g GENES --genes=GENES  a list of comma separated gene names (no spaces) [default: CAB11_002014]\n    -e EXCL --exc=EXCL      a quoted regular expression for effects to exclude [default: 'synonymous_variant']\n    -o OUT --out=OUT        csv or gz file to save output to [default: out.csv]\n    -h, --help              show this help text\n```\n\nTo set it up to run from anywhere in your environment, add the path to your .bashrc file:\n\n```\nexport PATH=$PATH:path/to/snpeffr.R\n```\n## Docker image\n\nThere is a docker image to run snpeffr [here](https://github.com/CDCgov/snpeffr/pkgs/container/snpeffr), built off of rocker/r-ver. \nIt moves the command line script to the top level. To run inside docker use:\n\n```\n# and other associated commands\n./snpeffr.R -h\n```\n\n## Next steps\n\n- Use [snpsift](https://github.com/nf-core/modules/tree/master/modules/nf-core/snpsift) to do some of the upstream filtering (should be faster than reading in the\nlarger vcf using data.table, currently only the split command is a module, so we would\nneed to set up the filter command as a module if we wanted to use this.)\n\n# CDCgov GitHub Organization Open Source Project\n\n**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm).  GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. \n\n## Related documents\n\n* [Open Practices](open_practices.md)\n* [Rules of Behavior](rules_of_behavior.md)\n* [Thanks and Acknowledgements](thanks.md)\n* [Disclaimer](DISCLAIMER.md)\n* [Contribution Notice](CONTRIBUTING.md)\n* [Code of Conduct](code-of-conduct.md)\n\n## Public Domain Standard Notice\nThis repository constitutes a work of the United States Government and is not\nsubject to domestic copyright protection under 17 USC § 105. This repository is in\nthe public domain within the United States, and copyright and related rights in\nthe work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).\nAll contributions to this repository will be released under the CC0 dedication. By\nsubmitting a pull request you are agreeing to comply with this waiver of\ncopyright interest.\n\n## License Standard Notice\nThe repository utilizes code licensed under the terms of the Apache Software\nLicense and therefore is licensed under ASL v2 or later.\n\nThis source code in this repository is free: you can redistribute it and/or modify it under\nthe terms of the Apache Software License version 2, or (at your option) any\nlater version.\n\nThis source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY\nWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\nPARTICULAR PURPOSE. See the Apache Software License for more details.\n\nYou should have received a copy of the Apache Software License along with this\nprogram. If not, see http://www.apache.org/licenses/LICENSE-2.0.html\n\nThe source code forked from other open source projects will inherit its license.\n\n## Privacy Standard Notice\nThis repository contains only non-sensitive, publicly available data and\ninformation. All material and community participation is covered by the\n[Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)\nand [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).\nFor more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).\n\n## Contributing Standard Notice\nAnyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)\nand submitting a pull request. (If you are new to GitHub, you might start with a\n[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing\nto this project, you grant a world-wide, royalty-free, perpetual, irrevocable,\nnon-exclusive, transferable license to all users under the terms of the\n[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or\nlater.\n\nAll comments, messages, pull requests, and other submissions received through\nCDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).\n\n## Records Management Standard Notice\nThis repository is not a source of government records, but is a copy to increase\ncollaboration and collaborative potential. All government records will be\npublished through the [CDC web site](http://www.cdc.gov).\n\n## Additional Standard Notices\nPlease refer to [CDC's Template Repository](https://github.com/CDCgov/template)\nfor more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),\n[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),\nand [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdcgov%2Fsnpeffr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcdcgov%2Fsnpeffr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdcgov%2Fsnpeffr/lists"}