{"id":18595554,"url":"https://github.com/pasted/simple_bash_pipeline","last_synced_at":"2026-05-20T07:40:18.512Z","repository":{"id":141567118,"uuid":"48800642","full_name":"pasted/simple_bash_pipeline","owner":"pasted","description":"Historical version of targeted panel sequencing pipeline for Monogenic Diabetes. 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Original Bash pipeline for Exeter Molecular Genetics Lab circa 2012-2013\n\nGATK Best practices pipeline with hard filtering on a given common sequencing artefacts and variants of no known clinical signficance. Since superceded by a Ruby based pipeline (after 2013).\n\n##### Example format for the sample_list.csv\n```\nCapture number,MODY number,EX number,Gender,Analysis,Disease,Sample type,Comment\np5_8_001,MY0000XX01,EX0000001,Male,MODY,MODY,Whole blood,positive control (1) HNF1A c.872dup/N\np5_8_002,MY0000YY02,EX0000003,Female,MODY,MODY,Whole blood,positive control (2) HNF1B delex1-9/N\n```\n##### Licence\n\n    Copyright (C) 2013 Garan Jones\n\n    This program is free software: you can redistribute it and/or modify\n    it under the terms of the GNU General Public License as published by\n    the Free Software Foundation, either version 3 of the License, or\n    (at your option) any later version.\n\n    This program is distributed in the hope that it will be useful,\n    but WITHOUT ANY WARRANTY; without even the implied warranty of\n    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n    GNU General Public License for more details.\n\n    You should have received a copy of the GNU General Public License\n    along with this program. If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpasted%2Fsimple_bash_pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpasted%2Fsimple_bash_pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpasted%2Fsimple_bash_pipeline/lists"}