{"id":17141480,"url":"https://github.com/iskandr/simple-somatic-variant-calling","last_synced_at":"2025-07-23T23:04:32.845Z","repository":{"id":138356700,"uuid":"130735161","full_name":"iskandr/simple-somatic-variant-calling","owner":"iskandr","description":"A simple genomics \"pipeline\" implemented via shell scripts","archived":false,"fork":false,"pushed_at":"2019-07-25T23:03:02.000Z","size":28,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-24T08:23:55.456Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/iskandr.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":"2018-04-23T17:50:49.000Z","updated_at":"2021-01-07T17:40:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"64460a34-8bdb-46b6-a7ea-6f85ebfc9870","html_url":"https://github.com/iskandr/simple-somatic-variant-calling","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/iskandr/simple-somatic-variant-calling","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iskandr%2Fsimple-somatic-variant-calling","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iskandr%2Fsimple-somatic-variant-calling/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iskandr%2Fsimple-somatic-variant-calling/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iskandr%2Fsimple-somatic-variant-calling/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/iskandr","download_url":"https://codeload.github.com/iskandr/simple-somatic-variant-calling/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/iskandr%2Fsimple-somatic-variant-calling/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266764645,"owners_count":23980602,"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":"2025-07-23T02:00:09.312Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":[],"created_at":"2024-10-14T20:25:31.996Z","updated_at":"2025-07-23T23:04:32.830Z","avatar_url":"https://github.com/iskandr.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# simple-somatic-variant-calling\nA simple genomics \"pipeline\" implemented via a single shell script. Aligns tumor \u0026 normal DNA sequencing data, marks duplicate reads in BAM files, and runs Strelka2 as a somatic variant caller. \n\nExpected input FASTQ files for normal and tumor DNA sequencing data. The pipeline will generate (in whichever directory it's invoked) a collection of BAM files and ultimately two VCFs: somatic SNVs and somatic indels. \n\n## Requirements\n\n * [sambamba](http://lomereiter.github.io/sambamba/)\n * [bamtools](https://github.com/pezmaster31/bamtools)\n * [Picard](https://broadinstitute.github.io/picard/)\n * [BWA](http://bio-bwa.sourceforge.net/)\n * [Strelka2](https://github.com/Illumina/strelka/)\n\n## Invocation \n```sh\n./call-somatic-variants $PATH_TO_NORMAL $NORMAL_FASTQ_PREFIX $PATH_TO_TUMOR $TUMOR_FASTQ_PREFIX\n```\n\nGenerates BAMs and VCF file in the directory it was invoked. You can edit the shell script to specify a directory with an indexed human reference, otherwise the reference gets downloaded and indexed in the same directory. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fiskandr%2Fsimple-somatic-variant-calling","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fiskandr%2Fsimple-somatic-variant-calling","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fiskandr%2Fsimple-somatic-variant-calling/lists"}