Commit 39fb9c11 authored by Pradat Yoann's avatar Pradat Yoann

update README

parent 038fa023
......@@ -45,13 +45,19 @@ Run the VEP annotator on the VCF file from a specific set of options. The option
## 2. How to run the tool ?
Clone the github repository using
```
git clone --recurse-submodules https://github.com/Durzot/BT_variant_annotator
```
or, if you forgot the `--recurse-submodules` option, run `git submodule update --init` after the cloning.
### 2.1 Install VEP
Clone VEP from the [official github](https://github.com/Ensembl/ensembl-vep). Installation details are provided there. As specified, run
Go to the ensembl-vep/ folder in tools/ and run
```
git clone https://github.com/Ensembl/ensembl-vep
cd ensembl-vep
perl INSTALL.pl
```
......@@ -99,7 +105,7 @@ You may replace `/usr/local/bin` with whatever path where you usually save binar
### 2.3 Example
The main function for annotating a vcf is `run_annotator` in `main` module. Have a look at `run_example_tcga_GA.py` to have an example of how to run the tool and at the `run_annotator` documentation for more details about the options.
The main function for annotating a vcf is `run_annotator` in `main` module. Have a look at `run_example_tcga_GA.py` or `run_example_tcga_HS` to have examples of how to run the tool and at the `run_annotator` documentation for more details about the options.
## 3. References
......
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