{"id":25905448,"url":"https://github.com/stevekm/mutect2_target_chunking","last_synced_at":"2026-01-30T21:02:34.895Z","repository":{"id":94518020,"uuid":"194908720","full_name":"stevekm/MuTect2_target_chunking","owner":"stevekm","description":"demo pipeline for testing different data chunking methods for MuTect2","archived":false,"fork":false,"pushed_at":"2019-07-02T17:53:26.000Z","size":162,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-06-13T20:06:08.053Z","etag":null,"topics":["mutect2","nextflow","variant-calling"],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","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/stevekm.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-07-02T17:40:07.000Z","updated_at":"2019-07-02T17:53:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"f5633df9-e59f-411d-9188-e7d4defa9732","html_url":"https://github.com/stevekm/MuTect2_target_chunking","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/stevekm/MuTect2_target_chunking","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FMuTect2_target_chunking","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FMuTect2_target_chunking/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FMuTect2_target_chunking/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FMuTect2_target_chunking/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stevekm","download_url":"https://codeload.github.com/stevekm/MuTect2_target_chunking/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FMuTect2_target_chunking/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28919362,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-30T20:25:28.696Z","status":"ssl_error","status_checked_at":"2026-01-30T20:25:13.426Z","response_time":66,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":["mutect2","nextflow","variant-calling"],"created_at":"2025-03-03T05:15:11.397Z","updated_at":"2026-01-30T21:02:34.890Z","avatar_url":"https://github.com/stevekm.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MuTect2 Target Chunking\n\nDemo pipeline for testing different data chunking methods for MuTect2.\n\n[MuTect2](https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php) is a common tool used for variant calling of tumor-normal pairs. However, it is limited to running only in single-threaded mode, which can lead to extremely long execution times. \n\nThis demo pipeline uses different techniques to chunk the included list of target regions (`targets.bed`) into smaller segments to run in parallel, then aggregate all results for comparison to ensure that variant calls are the same across all chunking methods.\n\n# Usage\n\nThis pipeline comes pre-configured for usage on NYULMC's Big Purple HPC cluster using pre-built Singularity containers and pre-downloaded reference files. \n\nIn order to use this pipeline on your system you will need to update the file paths saved in `nextflow.config` for your system. \n\nSingularity and Docker container recipes are included in the `containers` directory.\n\nPaths to input .bam files for tumor and normal samples are read from the file `samples.analysis.tsv`.\n\nOnce correctly configured, the pipeline can be run with:\n\n```\nmake run\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevekm%2Fmutect2_target_chunking","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstevekm%2Fmutect2_target_chunking","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevekm%2Fmutect2_target_chunking/lists"}