https://github.com/pasted/simple_bash_pipeline
Historical version of targeted panel sequencing pipeline for Monogenic Diabetes. Originally developed as Masters in Bioinformatics project @ University of Exeter
https://github.com/pasted/simple_bash_pipeline
bash bioinformatics-pipeline pipeline
Last synced: about 1 month ago
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Historical version of targeted panel sequencing pipeline for Monogenic Diabetes. Originally developed as Masters in Bioinformatics project @ University of Exeter
- Host: GitHub
- URL: https://github.com/pasted/simple_bash_pipeline
- Owner: pasted
- License: gpl-3.0
- Created: 2015-12-30T12:54:08.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2015-12-31T10:14:21.000Z (over 10 years ago)
- Last Synced: 2025-07-08T19:13:11.761Z (12 months ago)
- Topics: bash, bioinformatics-pipeline, pipeline
- Language: Ruby
- Homepage:
- Size: 41 KB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
#Simple BASH Pipeline
============================
Alignment and analysis pipeline for NHS targeted sequencing
Only for historical interest. Original Bash pipeline for Exeter Molecular Genetics Lab circa 2012-2013
GATK 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 Since superceded by a Ruby based pipeline (after 2013).
##### Example format for the sample_list.csv
```
Capture number,MODY number,EX number,Gender,Analysis,Disease,Sample type,Comment
p5_8_001,MY0000XX01,EX0000001,Male,MODY,MODY,Whole blood,positive control (1) HNF1A c.872dup/N
p5_8_002,MY0000YY02,EX0000003,Female,MODY,MODY,Whole blood,positive control (2) HNF1B delex1-9/N
```
##### Licence
Copyright (C) 2013 Garan Jones
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .