{"id":24360474,"url":"https://github.com/simonsfoundation/remap2b38","last_synced_at":"2025-07-24T12:38:34.755Z","repository":{"id":98237459,"uuid":"100283501","full_name":"simonsfoundation/remap2b38","owner":"simonsfoundation","description":"Remap a bam file to a given reference, and call variants with a choice of GATK HaplotypeCaller, Freebayes, Platypus.","archived":false,"fork":false,"pushed_at":"2017-08-22T20:05:52.000Z","size":12,"stargazers_count":0,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-18T21:32:28.260Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Shell","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/simonsfoundation.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":"2017-08-14T15:40:40.000Z","updated_at":"2017-08-14T17:01:39.000Z","dependencies_parsed_at":"2023-04-29T14:50:05.034Z","dependency_job_id":null,"html_url":"https://github.com/simonsfoundation/remap2b38","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fremap2b38","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fremap2b38/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fremap2b38/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fremap2b38/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/simonsfoundation","download_url":"https://codeload.github.com/simonsfoundation/remap2b38/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243188204,"owners_count":20250452,"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":"2025-01-18T21:29:52.261Z","updated_at":"2025-03-12T08:43:17.176Z","avatar_url":"https://github.com/simonsfoundation.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"## *remap2b38*\n\n### Overview\n\n*remap2b38* contains one script *remap.sh* that can be used to remap a bam file to \na new reference genome, and to call variants with a choice of GATK HaplotypeCaller,\nFreebayes, and Platypus using [*pipeline*](https://github.com/simonsfoundation/pipeline.git).\n\nThe following steps will be executed.\n\n    1. samtools collate\n    2. samtools fastq\n    3. bwa mem\n    3. sambamba sort\n    4. sambamba markdup\n    5. GATK base quality recalibrate\n    6. sambamba index\n    7. Call variants using pipeline\n\nIf you do not wish to call variants, comment out pipe04.sh call.\n\n### Dependences.\n\n[*samtools*](http://www.htslib.org) and [*sambamba*](http://lomereiter.github.io/sambamba/) must be in your $PATH.\n\nClone *pipeline*.\n```\ncd ~\ngit clone https://github.com/simonsfoundation/pipeline.git\n```   \n\nClone this repo\n```\ncd ~\ngit clone https://github.com/simonsfoundation/remap2b38.git\n```\n\nRun\n```\n~/remap2b38/remap.sh \\\n   bam_prefix \\ # eg 123, if bam(s) are 123*.bam\n   /path/to/iput_bams_dir/ \\ # directory containing files defined by the prefix\n   scr \\ # tmp/scr/work defines working dir, see comments in remap.sh\n   /path/to/output_dir/ \\ # output directory (will be created)\n   1 \\ # 1/0 remove working_dir/do not remove\n   8 \\ # use this many cores\n   /path/to/include_hg38.mk   \\ # e.g. ~/pipeline/ppln/include_hg38.mk, if you followed instructions above\n   /path/to/pipeline/ppln \\ # e.g. ~/, if you followed instructions above\n   \u003e /path/to/log_file.log 2\u003e\u00261\n```\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fremap2b38","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsimonsfoundation%2Fremap2b38","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fremap2b38/lists"}