{"id":13637836,"url":"https://github.com/broadinstitute/mutect","last_synced_at":"2025-04-19T17:32:18.363Z","repository":{"id":6650199,"uuid":"7894514","full_name":"broadinstitute/mutect","owner":"broadinstitute","description":"MuTect -- Accurate and sensitive cancer mutation detection","archived":false,"fork":false,"pushed_at":"2023-02-13T21:40:10.000Z","size":75663,"stargazers_count":92,"open_issues_count":11,"forks_count":45,"subscribers_count":43,"default_branch":"master","last_synced_at":"2024-02-15T09:33:35.593Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://www.broadinstitute.org/cancer/cga/mutect","language":"Java","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/broadinstitute.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,"governance":null}},"created_at":"2013-01-29T15:09:43.000Z","updated_at":"2024-01-22T10:05:51.000Z","dependencies_parsed_at":"2022-08-22T13:30:45.687Z","dependency_job_id":"48bfb855-6373-48c9-962c-b04030ec4e4e","html_url":"https://github.com/broadinstitute/mutect","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fmutect","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fmutect/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fmutect/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fmutect/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/mutect/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223804969,"owners_count":17205832,"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":[],"created_at":"2024-08-02T01:00:34.961Z","updated_at":"2024-11-09T08:30:24.169Z","avatar_url":"https://github.com/broadinstitute.png","language":"Java","readme":"Overview\n--------------------------------------------------------\nFor complete details see\n\nhttp://www.broadinstitute.org/cancer/cga/mutect\n\nAnd for support please visit\n\nhttp://gatkforums.broadinstitute.org/categories/mutect\n\n\nHow to build MuTect\n--------------------------------------------------------\n\nPREREQUISITES\n\nTo compile MuTect you must be using Java 1.7 and Maven 3.0+.  After building successfully, the MuTect JAR file will be in mutect/target/mutect-*.jar\n\nBUILD STEPS\n\n    # make a new source directory (e.g. mutect-src)\n    mkdir mutect-src\n    cd mutect-src\n\n    # get MuTect source\n    git clone git@github.com:broadinstitute/mutect.git\n\n    # get the GATK source and set to the latest tested version\n    git clone git@github.com:broadgsa/gatk-protected.git\n    cd gatk-protected\n    git reset --hard 3.1 \n    \n    # build the GATK first and install it to the local mvn repo.  Once GATK publishes to a public repo this will be much simpler\n    mvn -Ddisable.queue install\n\n\t# build MuTect and run unit tests (the target jar will be in target/mutect-*.jar)\n\tcd ../mutect\n\tmvn verify\n\t\n\t# run integration tests, if you like\n\t./run_regression.pl\n\t./tieout_regression.pl\n\n","funding_links":[],"categories":["Variant Callers","Genomics"],"sub_categories":["Somatic SNV/Indel callers","Mutations"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbroadinstitute%2Fmutect","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbroadinstitute%2Fmutect","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbroadinstitute%2Fmutect/lists"}