{"id":15704342,"url":"https://github.com/poisonalien/basecounts","last_synced_at":"2025-10-14T21:13:05.174Z","repository":{"id":182576269,"uuid":"266552951","full_name":"PoisonAlien/basecounts","owner":"PoisonAlien","description":"A tool to extract ATGC/Indel read counts at user specific loci from BAM files","archived":false,"fork":false,"pushed_at":"2022-02-22T09:54:02.000Z","size":39,"stargazers_count":5,"open_issues_count":1,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-05-12T16:53:30.562Z","etag":null,"topics":["bam","basecounts","bioinformatics","nucleotide-frequency","readcounts","sequencing","wgs-data"],"latest_commit_sha":null,"homepage":"","language":"C","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/PoisonAlien.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":"2020-05-24T14:02:15.000Z","updated_at":"2023-11-26T00:28:08.000Z","dependencies_parsed_at":null,"dependency_job_id":"713aa949-87c6-421b-b6d3-7dea85be4a57","html_url":"https://github.com/PoisonAlien/basecounts","commit_stats":null,"previous_names":["poisonalien/basecounts"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/PoisonAlien/basecounts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fbasecounts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fbasecounts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fbasecounts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fbasecounts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PoisonAlien","download_url":"https://codeload.github.com/PoisonAlien/basecounts/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fbasecounts/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279021378,"owners_count":26087020,"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","status":"online","status_checked_at":"2025-10-14T02:00:06.444Z","response_time":60,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["bam","basecounts","bioinformatics","nucleotide-frequency","readcounts","sequencing","wgs-data"],"created_at":"2024-10-03T20:11:27.516Z","updated_at":"2025-10-14T21:13:05.158Z","avatar_url":"https://github.com/PoisonAlien.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"## basecounts\n\n`basecounts` is a simple tool to extract nucleotide counts from BAM files for the user specific loci. This tool can also be used to generate VAF table for known somatic varaints without the proper variant calling. \n\n### Installation\n\nClone the repository and run `make`. Requires [htslib](https://github.com/samtools/htslib). \n\n```\ngit clone https://github.com/PoisonAlien/basecounts\ncd basecounts\nmake\n```\n\n```\n$ basecounts\n-------------------------------------------------------------------------\nbasecounts: A tool to extract nucleotide counts\n            of genomic loci from the BAM file. Version: 0.1.0\nUSAGE:\n    basecounts [OPTIONS] \u003cloci\u003e \u003cbam\u003e\n    e.g; basecounts target_loci.tsv Tumor.bam\nOPTIONS:\n    -f  Indexed fasta file. If provided, extracts and adds reference base to the ouput tsv\n    -q  Min. mapping quality threshold. Default 10 [Read filter]\n    -F  Exclude reads with FLAGS \u003e= INT. Default 3852 [Read filter]\n    -o  Output file basename. Default parses from basename of BAM file\nARGS:\n    \u003cloci\u003e   loci file (chr\\tpos)\n    \u003cbam\u003e    Indexed BAM file\nOUPUT:\n    \u003coutput\u003e.tsv    TSV file with nucletide counts for all variants\n-------------------------------------------------------------------------\n\n```\n\n### Usage\n\n`basecounts` takes a 2 column tsv file with loci and the sorted/indexed BAM file as positional arguments.\n\n\nFirst two columns of loci file should be chromsome and position.\n```\n$ head loci.tsv\n1\t6304615\n1\t10407830\n1\t46269731\n1\t47133825\n1\t50884996\n1\t84662414\n1\t152328587\n1\t216019313\n1\t226252155\n```\n\n```\n#basic usage\n$ basecounts loci.tsv tumor.bam \n\n#providing fasta file will add the reference base at the loci\n$ basecounts -f GRCh37.fa loci.tsv tumor.bam \n\n#Output is a TSV file with readcounts suporting all 4 nucleotide bases and INDELS\n$ head tumor.tsv \nloci    fa_ref  A       T       G       C       Ins     Del\n1:6304615       A       70      0       0       19      0       0\n1:10407830      C       0       0       39      50      0       0\n1:46269731      A       50      3       1       21      0       0\n1:47133825      T       3       37      14      4       0       0\n1:50884996      A       51      0       0       15      0       0\n1:84662414      G       0       2       81      0       0       0\n1:152328587     A       85      3       0       0       0       0\n1:216019313     T       0       53      17      0       0       0\n1:226252155     G       0       41      52      0       0       0\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fbasecounts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpoisonalien%2Fbasecounts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fbasecounts/lists"}