{"id":13704056,"url":"https://github.com/AndersenLab/bam-toolbox","last_synced_at":"2025-05-05T09:32:53.670Z","repository":{"id":70156365,"uuid":"45126755","full_name":"AndersenLab/bam-toolbox","owner":"AndersenLab","description":"A bam toolbox","archived":false,"fork":false,"pushed_at":"2024-07-30T17:47:33.000Z","size":1853,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":10,"default_branch":"master","last_synced_at":"2024-08-03T21:04:33.320Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/AndersenLab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-10-28T16:36:51.000Z","updated_at":"2024-07-30T17:47:36.000Z","dependencies_parsed_at":"2024-01-03T06:47:45.021Z","dependency_job_id":"a3c1463e-5edf-4bc5-b381-3016e5d8dd00","html_url":"https://github.com/AndersenLab/bam-toolbox","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AndersenLab%2Fbam-toolbox","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AndersenLab%2Fbam-toolbox/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AndersenLab%2Fbam-toolbox/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AndersenLab%2Fbam-toolbox/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AndersenLab","download_url":"https://codeload.github.com/AndersenLab/bam-toolbox/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224439681,"owners_count":17311501,"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":"2024-08-02T21:01:03.588Z","updated_at":"2024-11-13T11:30:43.381Z","avatar_url":"https://github.com/AndersenLab.png","language":"Python","funding_links":[],"categories":["Next Generation Sequencing"],"sub_categories":["BAM File Utilities"],"readme":"# bam-toolbox\n\n## Installation\n\n```\npip install https://github.com/AndersenLab/bam-toolbox/archive/1.0.0.tar.gz\n```\n\n## Usage\n\n    bam-toolbox 1.0\n\n    usage:\n      bam \u003ccommand\u003e [\u003cargs\u003e...]\n      bam -h | --help\n      bam --version\n\n    commands:\n      coverage\n\n## Commands\n\n### Coverage\n\nCalculate depth of coverage! There are several ways to do so:\n\n1. Calculate coverage for the whole genome, nuclear genome, and individual chromosomes. Also calculated the mtDNA:nuclear ratio which acts as a proxy for mitochondrial content.\n\n2.\n\n```\nusage:\n  bam coverage \u003cbam\u003e [options] [--mtchr=\u003cmtchr\u003e]\n  bam coverage \u003cbam\u003e [options] \u003cchrom:start-end\u003e...\n  bam coverage \u003cbam\u003e [options] --window=\u003csize\u003e\n  bam coverage \u003cbam\u003e [options] --regions=\u003cgff/bed\u003e\n```\n\n###### Parameters\n\n* `--header` - Output the header line.\n* `--mtchr` - Specifying a mitochondrial chromosome will output the mtDNA:nuclear DNA ratio, offering an estimate of mitochondrial content. \n* `--window` - Calculate depth of coverage for given windows across the genome.\n* `--regions` - Specify a bed or gff file and calculate coverage in those regions.\n\n###### Example\n\n```\nbam coverage test.bam --tsv --header\n```\n\n__Result:__\n\nOutput is in `--tsv` format.\n\n```\nENTITY  chrom   start   end ATTR    VALUE   DATE\nCB4853  I   1   15072434    bases_mapped    1688210 2015-11-08 23:22:39.498133\nCB4853  I   1   15072434    depth_of_coverage   0.112006461597  2015-11-08 23:22:39.498242\nCB4853  I   1   15072434    breadth_of_coverage 0.0918075342045 2015-11-08 23:22:39.498328\nCB4853  I   1   15072434    length  15072434    2015-11-08 23:22:39.498372\nCB4853  I   1   15072434    pos_mapped  1383763 2015-11-08 23:22:39.498413\nCB4853  II  1   15279421    bases_mapped    1605336 2015-11-08 23:22:39.923802\nCB4853  II  1   15279421    depth_of_coverage   0.105065237747  2015-11-08 23:22:39.923880\n...\nCB4853  mt_nuclear_ratio    51.7503772943   2015-11-08 23:22:41.949819\n```\n\n__Formatted Result:__\n\n| ENTITY   | chrom   |   start |      end | ATTR                |       VALUE | DATE                       |\n|:---------|:--------|--------:|---------:|:--------------------|------------:|:---------------------------|\n| CB4853   | I       |       1 | 15072434 | bases_mapped        | 1.68821e+06 | 2015-11-08 23:26:41.891988 |\n| CB4853   | I       |       1 | 15072434 | depth_of_coverage   | 0.112006    | 2015-11-08 23:26:41.892087 |\n| CB4853   | I       |       1 | 15072434 | breadth_of_coverage | 0.0918075   | 2015-11-08 23:26:41.892155 |\n| CB4853   | I       |       1 | 15072434 | length              | 1.50724e+07 | 2015-11-08 23:26:41.892198 |\n| CB4853   | I       |       1 | 15072434 | pos_mapped          | 1.38376e+06 | 2015-11-08 23:26:41.892239 |\n| CB4853   | II      |       1 | 15279421 | bases_mapped        | 1.60534e+06 | 2015-11-08 23:26:42.319937 |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAndersenLab%2Fbam-toolbox","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FAndersenLab%2Fbam-toolbox","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAndersenLab%2Fbam-toolbox/lists"}