README.md

# STR detection pipeline

- ASDP PIPELINE
- Author: anne-sophie.denomme-pichon@u-bourgogne.fr
- Version: 0.0.1
- Licence: AGPLv3
- Description: How to launch scripts to get STR genotype from genomes on all the locus tested

1. Create `samples.list`
2. Fill the configuration file `config.sh`. Warning, don't overwrite existing files
3. Launch `launch_pipeline.sh` : `nohup ./launch_pipeline.sh samples.list &`. Dependencies :
   - `config.sh`
   - `samples.list`
   - `pipeline.sh`
   - `wrapper_delete.sh`
   - `wrapper_ehdn.sh`
   - `wrapper_expansionhunter.sh`
   - `wrapper_gangstr.sh`
   - `wrapper_transfer.sh`
   - `wrapper_tredparse.sh`
4. Launch `launch_pipeline_ehdn_outlier.sh` : `nohup ./launch_pipeline_ehdn_outlier.sh &`. Dependencies :
   - `config.sh`
   - `pipeline_ehdn_outlier.sh`
   - `wrapper_ehdn_outlier.sh`
5. Launch `getResults.py`. Warning, don't overwrite existing files.
6. Launch `launch_str_plotly.sh`.
7. Change z-score threshold if necessary in `config.sh`. Launch `launch_str_outliers.sh`. Dependency: `patho.csv`.
10. Get files (i.e.: `scp 'an1770de@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`)