Update README

README.md

-# STR detection pipeline
+# GAD STR expansion detection pipeline
 
-- ASDP PIPELINE
-- Author:  Anne-Sophie Denommé-Pichon
-- Version: 0.0.1
-- Licence: AGPLv3
-- Description: How to launch scripts to get STR genotype from genomes on all the locus tested
+ - Author:  Anne-Sophie Denommé-Pichon
+ - Version: 0.0.1
+ - Licence: AGPLv3
+ - Description: this pipeline allows to get STR genotype from short-read genomes on the locus specified. It uses ExpansionHunter, Tredparse and GangSTR. It computes genotypes called by the tools and identifies STR expansions using 3 outlier detection methods to highlight abnormal repeat counts.
 
-1. Fill the configuration file `config.sh`.
-2. Create `samples.list` (bam file names without .bam).
+## Setup
+
+ - Fill the configuration file `config.sh`. There is an example in the repository.
+ - Create `samples.list` (bam file names without .bam). There is an example in the repository.
+
+## Usage
 
 For now, scripts have to be launched from the clone directory.
-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. Optional: launch `launch_pipeline_ehdn_outlier.sh`: `nohup ./launch_pipeline_ehdn_outlier.sh samples.list &`. Dependencies:
-   - `config.sh`
-   - `samples.list`
-   - `pipeline_ehdn_outlier.sh`
-   - `wrapper_ehdn_outlier.sh`
-5. Launch `launch_results.sh`: `nohup ./launch_results.sh samples.list &`. Dependencies:
-   - `config.sh`
-   - `samples.list`
-   - `patho.csv`
-   - `getResults.py`
-   - `launch_str_outliers.sh`
-   - `str_outliers.py`
-6. Optional: launch `launch_str_plotly.sh`.
-7. Get files (i.e.: `scp 'username@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`)
 
+### Calling STRs
+
+Launch `launch_pipeline.sh`:
+
+```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`
+
+### Identifying outliers 
+
+To highlight abnormal repeat counts, the pipeline identified outliers using 3 methods: repeats counts at a given locus
+ 1. > normal (in the gray zone or pathological zone)
+ 2. > 99th percentile or
+ 3. ≥ 4 standard deviations above the mean (Z-score ≥ 4). 
+
+Launch `launch_results.sh`:
+
+```sh
+nohup ./launch_results.sh samples.list &
+```
+
+Dependencies:
+ - `config.sh`
+ - `samples.list`
+ - `patho.csv`
+ - `getResults.py`
+ - `launch_str_outliers.sh`
+ - `str_outliers.py`
+
+## Future work
+
+Another tool, ExpansionHunter DeNovo, will be added in the pipeline.