{"id":16619429,"url":"https://github.com/tomwhite/bamreport","last_synced_at":"2025-10-17T08:14:06.605Z","repository":{"id":66918090,"uuid":"128195380","full_name":"tomwhite/bamreport","owner":"tomwhite","description":"Produce a report on a BAM file listing useful information","archived":false,"fork":false,"pushed_at":"2018-04-05T11:15:08.000Z","size":119,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-17T21:43:53.335Z","etag":null,"topics":["bam","bioinformatics","genomics","ngs"],"latest_commit_sha":null,"homepage":null,"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/tomwhite.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}},"created_at":"2018-04-05T11:14:55.000Z","updated_at":"2018-06-17T20:17:05.000Z","dependencies_parsed_at":"2023-05-14T00:45:33.803Z","dependency_job_id":null,"html_url":"https://github.com/tomwhite/bamreport","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/tomwhite%2Fbamreport","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomwhite%2Fbamreport/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomwhite%2Fbamreport/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomwhite%2Fbamreport/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tomwhite","download_url":"https://codeload.github.com/tomwhite/bamreport/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242988047,"owners_count":20217539,"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":["bam","bioinformatics","genomics","ngs"],"created_at":"2024-10-12T02:25:23.727Z","updated_at":"2025-10-17T08:14:06.525Z","avatar_url":"https://github.com/tomwhite.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n```\nBAM=/Users/tom/workspace/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam\n~/sw/bedtools2/bin/bedtools genomecov -ibam $BAM -bga \u003e bam.bedgraph\n```\n\nFrom http://seqanswers.com/forums/showpost.php?p=116995\u0026postcount=11\n\n```\nDICT=/Users/tom/workspace/gatk/src/test/resources/large/human_g1k_v37.20.21.dict\ngrep '@SQ' $DICT | tr ':' '\\t' | awk -v OFS='\\t' '{print $3, $5}' \u003e $DICT.genome\n~/sw/bedtools2/bin/bedtools makewindows -g $DICT.genome -w 1000000 \\\n    | ~/sw/bedtools2/bin/bedtools coverage -a - -b $BAM -counts \u003e $BAM.counts.txt\n````\n\n\nbedtools coverage -hist -abam $BAM\n\n----\n\n```bash\nmvn compile\nmvn exec:java  -Dexec.mainClass=com.cloudera.bamreport.BamReport -Dexec.args=\"/Users/tom/workspace/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam\"\n\n\n# unmapped BAM\nmvn exec:java  -Dexec.mainClass=com.cloudera.bamreport.BamReport -Dexec.args=\"/Users/tom/workspace/gatk/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/QualityScoreDistribution/unmapped.bam\"\n```\n\nSparklines\n\n```bash\nmvn compile\nmvn -q exec:java  -Dexec.mainClass=com.cloudera.bamreport.BamCoverageSparkline -Dexec.args=\"/Users/tom/workspace/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam\" \u003e sparkline.html\nopen sparkline.html\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomwhite%2Fbamreport","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftomwhite%2Fbamreport","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomwhite%2Fbamreport/lists"}